Starting phenix.real_space_refine on Tue Apr 9 05:17:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2024/8hr7_34962.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2024/8hr7_34962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2024/8hr7_34962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2024/8hr7_34962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2024/8hr7_34962.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hr7_34962/04_2024/8hr7_34962.pdb" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 601 5.16 5 C 77620 2.51 5 N 21081 2.21 5 O 22360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 760": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C GLU 638": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 572": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "F GLU 354": "OE1" <-> "OE2" Residue "F GLU 671": "OE1" <-> "OE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 229": "OE1" <-> "OE2" Residue "G GLU 566": "OE1" <-> "OE2" Residue "G GLU 736": "OE1" <-> "OE2" Residue "I GLU 354": "OE1" <-> "OE2" Residue "I GLU 736": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J GLU 566": "OE1" <-> "OE2" Residue "J GLU 736": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K GLU 331": "OE1" <-> "OE2" Residue "K GLU 736": "OE1" <-> "OE2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 608": "OE1" <-> "OE2" Residue "L GLU 678": "OE1" <-> "OE2" Residue "M GLU 39": "OE1" <-> "OE2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "M GLU 289": "OE1" <-> "OE2" Residue "M GLU 704": "OE1" <-> "OE2" Residue "M GLU 785": "OE1" <-> "OE2" Residue "N GLU 472": "OE1" <-> "OE2" Residue "N GLU 760": "OE1" <-> "OE2" Residue "N GLU 785": "OE1" <-> "OE2" Residue "O GLU 202": "OE1" <-> "OE2" Residue "O GLU 545": "OE1" <-> "OE2" Residue "O GLU 638": "OE1" <-> "OE2" Residue "P GLU 890": "OE1" <-> "OE2" Residue "Q TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 471": "OE1" <-> "OE2" Residue "Q GLU 526": "OE1" <-> "OE2" Residue "Q GLU 534": "OE1" <-> "OE2" Residue "R GLU 209": "OE1" <-> "OE2" Residue "R PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 714": "OE1" <-> "OE2" Residue "S GLU 209": "OE1" <-> "OE2" Residue "S GLU 279": "OE1" <-> "OE2" Residue "S GLU 517": "OE1" <-> "OE2" Residue "T GLU 202": "OE1" <-> "OE2" Time to flip residues: 0.28s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 121662 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "B" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 6244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 6244 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 41, 'TRANS': 732} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 6217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6217 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 41, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6239 Classifications: {'peptide': 775} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 733} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "I" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "J" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "K" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6273 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 737} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "L" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 6361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6361 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 43, 'TRANS': 742} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 6247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6247 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 41, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "O" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "P" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "Q" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "R" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "S" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Chain: "T" Number of atoms: 6657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6657 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 6 Time building chain proxies: 44.56, per 1000 atoms: 0.37 Number of scatterers: 121662 At special positions: 0 Unit cell: (217.36, 303.68, 214.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 601 16.00 O 22360 8.00 N 21081 7.00 C 77620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.23 Conformation dependent library (CDL) restraints added in 15.6 seconds 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 28866 Finding SS restraints... Secondary structure from input PDB file: 737 helices and 88 sheets defined 62.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.31 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.663A pdb=" N TYR A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 140 removed outlier: 3.572A pdb=" N MET A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 169 removed outlier: 3.745A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.232A pdb=" N TYR A 189 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 removed outlier: 4.067A pdb=" N ILE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 241 removed outlier: 3.503A pdb=" N ARG A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.589A pdb=" N LEU A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.537A pdb=" N ASP A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.569A pdb=" N ASP A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 395 Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.971A pdb=" N GLY A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 432 Processing helix chain 'A' and resid 437 through 441 removed outlier: 4.080A pdb=" N PHE A 441 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 458 removed outlier: 3.928A pdb=" N LEU A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N CYS A 447 " --> pdb=" O MET A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.530A pdb=" N TYR A 465 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.524A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 514 removed outlier: 4.216A pdb=" N CYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 539 removed outlier: 3.530A pdb=" N ILE A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 560 removed outlier: 3.881A pdb=" N ARG A 553 " --> pdb=" O HIS A 549 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A 554 " --> pdb=" O TRP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 622 through 636 removed outlier: 3.686A pdb=" N ILE A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 705 through 722 removed outlier: 4.289A pdb=" N ALA A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 727 removed outlier: 3.747A pdb=" N GLY A 726 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 727 " --> pdb=" O GLU A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 727' Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.905A pdb=" N ASN A 746 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASN A 747 " --> pdb=" O PHE A 743 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 770 through 791 removed outlier: 3.507A pdb=" N ILE A 774 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 786 " --> pdb=" O PHE A 782 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.656A pdb=" N LYS A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 removed outlier: 3.674A pdb=" N SER A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 889 through 897 removed outlier: 4.663A pdb=" N LEU A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 25 through 41 removed outlier: 4.037A pdb=" N SER B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 63 Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 91 through 103 removed outlier: 4.644A pdb=" N SER B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLU B 97 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.613A pdb=" N SER B 123 " --> pdb=" O GLY B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.622A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 184 removed outlier: 3.774A pdb=" N ALA B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 200 through 224 Processing helix chain 'B' and resid 229 through 234 removed outlier: 3.713A pdb=" N ALA B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.517A pdb=" N ALA B 241 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B 242 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 331 through 343 Processing helix chain 'B' and resid 362 through 385 Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.982A pdb=" N LEU B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL B 407 " --> pdb=" O ASN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 456 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 479 through 490 removed outlier: 4.541A pdb=" N LEU B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 520 Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.604A pdb=" N GLY B 535 " --> pdb=" O CYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 574 through 593 removed outlier: 3.510A pdb=" N LYS B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 619 Processing helix chain 'B' and resid 632 through 647 removed outlier: 4.219A pdb=" N THR B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 662 Processing helix chain 'B' and resid 662 through 671 removed outlier: 3.534A pdb=" N ALA B 670 " --> pdb=" O ARG B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 700 Processing helix chain 'B' and resid 718 through 722 Processing helix chain 'B' and resid 723 through 729 removed outlier: 3.619A pdb=" N TRP B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 771 Processing helix chain 'B' and resid 775 through 793 removed outlier: 3.875A pdb=" N ARG B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 17 removed outlier: 3.658A pdb=" N THR C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 45 through 63 Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 94 through 103 removed outlier: 3.544A pdb=" N THR C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 118 Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.804A pdb=" N GLN C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 162 through 171 removed outlier: 4.041A pdb=" N LEU C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 removed outlier: 3.601A pdb=" N ALA C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 200 through 224 removed outlier: 3.564A pdb=" N ARG C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 243 removed outlier: 4.184A pdb=" N ASN C 242 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 280 removed outlier: 4.115A pdb=" N GLU C 269 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE C 270 " --> pdb=" O GLN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 309 Processing helix chain 'C' and resid 332 through 343 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.572A pdb=" N MET C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 371 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 406 Processing helix chain 'C' and resid 436 through 455 Processing helix chain 'C' and resid 456 through 462 Processing helix chain 'C' and resid 476 through 479 removed outlier: 3.505A pdb=" N LEU C 479 " --> pdb=" O PRO C 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 479' Processing helix chain 'C' and resid 480 through 489 Processing helix chain 'C' and resid 505 through 520 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 553 through 566 Processing helix chain 'C' and resid 574 through 593 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 632 through 648 removed outlier: 3.767A pdb=" N ARG C 639 " --> pdb=" O GLU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.639A pdb=" N SER C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 670 removed outlier: 3.741A pdb=" N ALA C 670 " --> pdb=" O ARG C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 700 Processing helix chain 'C' and resid 718 through 722 removed outlier: 3.692A pdb=" N GLU C 721 " --> pdb=" O ASN C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 729 removed outlier: 3.623A pdb=" N TRP C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 771 removed outlier: 3.542A pdb=" N LEU C 768 " --> pdb=" O LEU C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 793 removed outlier: 4.266A pdb=" N VAL C 786 " --> pdb=" O LYS C 782 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY C 790 " --> pdb=" O VAL C 786 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.761A pdb=" N LEU D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 17 removed outlier: 3.536A pdb=" N THR D 17 " --> pdb=" O TYR D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 41 Processing helix chain 'D' and resid 45 through 62 Processing helix chain 'D' and resid 68 through 80 removed outlier: 3.869A pdb=" N ARG D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 removed outlier: 3.549A pdb=" N THR D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 103 " --> pdb=" O GLN D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 120 through 124 removed outlier: 3.502A pdb=" N SER D 123 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 161 through 171 removed outlier: 3.607A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 185 removed outlier: 4.108A pdb=" N SER D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 196 removed outlier: 3.561A pdb=" N ALA D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 224 removed outlier: 3.724A pdb=" N VAL D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 242 removed outlier: 4.268A pdb=" N ASN D 242 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 280 Processing helix chain 'D' and resid 285 through 311 Processing helix chain 'D' and resid 331 through 343 removed outlier: 3.814A pdb=" N LEU D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 385 removed outlier: 4.062A pdb=" N LYS D 368 " --> pdb=" O ASN D 364 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 371 " --> pdb=" O GLN D 367 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS D 384 " --> pdb=" O TYR D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 removed outlier: 3.521A pdb=" N VAL D 400 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 456 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 479 through 489 removed outlier: 4.562A pdb=" N LEU D 483 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 520 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 553 through 568 removed outlier: 3.649A pdb=" N ARG D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 593 removed outlier: 3.622A pdb=" N LYS D 590 " --> pdb=" O ARG D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 609 through 612 Processing helix chain 'D' and resid 613 through 618 Processing helix chain 'D' and resid 632 through 647 Processing helix chain 'D' and resid 650 through 662 Processing helix chain 'D' and resid 662 through 669 Processing helix chain 'D' and resid 681 through 700 removed outlier: 3.626A pdb=" N ALA D 697 " --> pdb=" O MET D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 722 Processing helix chain 'D' and resid 723 through 729 Processing helix chain 'D' and resid 756 through 771 Processing helix chain 'D' and resid 775 through 793 removed outlier: 3.545A pdb=" N VAL D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG D 791 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 17 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 45 through 63 removed outlier: 3.703A pdb=" N ARG E 63 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 94 through 103 removed outlier: 3.562A pdb=" N SER E 103 " --> pdb=" O GLN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 118 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.506A pdb=" N LEU E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 184 Processing helix chain 'E' and resid 185 through 196 removed outlier: 3.512A pdb=" N LYS E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA E 193 " --> pdb=" O LYS E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 224 removed outlier: 3.553A pdb=" N VAL E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 removed outlier: 3.523A pdb=" N ALA E 232 " --> pdb=" O GLU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 243 removed outlier: 4.160A pdb=" N ASN E 242 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 279 Processing helix chain 'E' and resid 285 through 310 Processing helix chain 'E' and resid 330 through 343 Processing helix chain 'E' and resid 362 through 385 removed outlier: 3.664A pdb=" N LYS E 368 " --> pdb=" O ASN E 364 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS E 384 " --> pdb=" O TYR E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 407 removed outlier: 3.540A pdb=" N LEU E 401 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL E 407 " --> pdb=" O ASN E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 456 removed outlier: 4.090A pdb=" N MET E 452 " --> pdb=" O ILE E 448 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 453 " --> pdb=" O LEU E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 removed outlier: 3.627A pdb=" N GLY E 461 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 479 Processing helix chain 'E' and resid 480 through 489 removed outlier: 3.553A pdb=" N VAL E 486 " --> pdb=" O PRO E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 520 Processing helix chain 'E' and resid 531 through 536 removed outlier: 3.647A pdb=" N GLY E 535 " --> pdb=" O CYS E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 543 removed outlier: 3.938A pdb=" N ARG E 543 " --> pdb=" O SER E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 568 removed outlier: 3.556A pdb=" N ARG E 568 " --> pdb=" O TRP E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 593 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 610 through 612 No H-bonds generated for 'chain 'E' and resid 610 through 612' Processing helix chain 'E' and resid 613 through 619 Processing helix chain 'E' and resid 632 through 647 Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 662 through 670 Processing helix chain 'E' and resid 681 through 700 Processing helix chain 'E' and resid 723 through 729 Processing helix chain 'E' and resid 756 through 771 Processing helix chain 'E' and resid 775 through 793 Processing helix chain 'F' and resid 1 through 6 Processing helix chain 'F' and resid 8 through 18 Processing helix chain 'F' and resid 25 through 41 Processing helix chain 'F' and resid 45 through 63 removed outlier: 3.711A pdb=" N ARG F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 94 through 103 Processing helix chain 'F' and resid 107 through 118 Processing helix chain 'F' and resid 120 through 124 removed outlier: 3.583A pdb=" N GLN F 124 " --> pdb=" O PRO F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'F' and resid 163 through 171 Processing helix chain 'F' and resid 171 through 184 removed outlier: 3.530A pdb=" N ALA F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 196 removed outlier: 3.597A pdb=" N LYS F 189 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 224 removed outlier: 3.578A pdb=" N VAL F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 234 Processing helix chain 'F' and resid 236 through 242 removed outlier: 4.116A pdb=" N ASN F 242 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 280 Processing helix chain 'F' and resid 285 through 310 removed outlier: 3.539A pdb=" N TRP F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 343 Processing helix chain 'F' and resid 362 through 385 removed outlier: 3.778A pdb=" N MET F 366 " --> pdb=" O ASP F 362 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 405 removed outlier: 3.546A pdb=" N VAL F 400 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 456 removed outlier: 3.544A pdb=" N LEU F 449 " --> pdb=" O GLN F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 462 Processing helix chain 'F' and resid 476 through 479 Processing helix chain 'F' and resid 480 through 489 Processing helix chain 'F' and resid 505 through 520 Processing helix chain 'F' and resid 531 through 536 Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 553 through 568 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 573 through 593 removed outlier: 3.748A pdb=" N ALA F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 585 " --> pdb=" O ALA F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 613 through 619 Processing helix chain 'F' and resid 632 through 647 removed outlier: 3.551A pdb=" N ARG F 641 " --> pdb=" O TYR F 637 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 643 " --> pdb=" O ARG F 639 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL F 644 " --> pdb=" O ALA F 640 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR F 647 " --> pdb=" O LEU F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.532A pdb=" N LEU F 653 " --> pdb=" O MET F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 669 Processing helix chain 'F' and resid 681 through 699 removed outlier: 3.656A pdb=" N ARG F 699 " --> pdb=" O LYS F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 728 removed outlier: 3.554A pdb=" N TRP F 727 " --> pdb=" O HIS F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 756 through 770 Processing helix chain 'F' and resid 775 through 793 removed outlier: 3.934A pdb=" N ARG F 781 " --> pdb=" O ALA F 777 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU F 785 " --> pdb=" O ARG F 781 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL F 786 " --> pdb=" O LYS F 782 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY F 790 " --> pdb=" O VAL F 786 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG F 791 " --> pdb=" O ASN F 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 8 through 17 Processing helix chain 'G' and resid 25 through 41 removed outlier: 3.520A pdb=" N SER G 31 " --> pdb=" O GLU G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 62 removed outlier: 3.540A pdb=" N LYS G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 94 through 103 Processing helix chain 'G' and resid 107 through 118 Processing helix chain 'G' and resid 120 through 124 removed outlier: 3.545A pdb=" N SER G 123 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 146 removed outlier: 3.558A pdb=" N ASP G 141 " --> pdb=" O PRO G 137 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR G 142 " --> pdb=" O THR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 171 removed outlier: 3.599A pdb=" N TRP G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 184 removed outlier: 3.757A pdb=" N ALA G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 196 Processing helix chain 'G' and resid 200 through 224 Processing helix chain 'G' and resid 229 through 234 Processing helix chain 'G' and resid 236 through 241 removed outlier: 3.563A pdb=" N LEU G 240 " --> pdb=" O PRO G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 280 removed outlier: 3.567A pdb=" N LYS G 279 " --> pdb=" O GLY G 275 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP G 280 " --> pdb=" O LEU G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 310 removed outlier: 4.306A pdb=" N ASP G 310 " --> pdb=" O LEU G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 343 removed outlier: 3.642A pdb=" N LEU G 335 " --> pdb=" O GLU G 331 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE G 338 " --> pdb=" O TYR G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 385 Processing helix chain 'G' and resid 396 through 406 removed outlier: 3.732A pdb=" N LEU G 406 " --> pdb=" O ASP G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 456 removed outlier: 3.864A pdb=" N MET G 452 " --> pdb=" O ILE G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 462 removed outlier: 3.958A pdb=" N GLY G 461 " --> pdb=" O ARG G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 479 Processing helix chain 'G' and resid 480 through 490 Processing helix chain 'G' and resid 505 through 520 Processing helix chain 'G' and resid 531 through 536 removed outlier: 3.566A pdb=" N GLY G 535 " --> pdb=" O CYS G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 553 through 568 Processing helix chain 'G' and resid 573 through 593 removed outlier: 4.229A pdb=" N ALA G 577 " --> pdb=" O LEU G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 609 Processing helix chain 'G' and resid 610 through 612 No H-bonds generated for 'chain 'G' and resid 610 through 612' Processing helix chain 'G' and resid 613 through 619 removed outlier: 3.540A pdb=" N GLY G 618 " --> pdb=" O ALA G 614 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU G 619 " --> pdb=" O GLU G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 632 through 647 removed outlier: 3.681A pdb=" N GLU G 638 " --> pdb=" O LEU G 634 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA G 640 " --> pdb=" O GLU G 636 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG G 641 " --> pdb=" O TYR G 637 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR G 647 " --> pdb=" O LEU G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 661 Processing helix chain 'G' and resid 662 through 671 Processing helix chain 'G' and resid 681 through 700 removed outlier: 3.661A pdb=" N LYS G 695 " --> pdb=" O ALA G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 718 through 722 removed outlier: 3.703A pdb=" N GLU G 721 " --> pdb=" O ASN G 718 " (cutoff:3.500A) Processing helix chain 'G' and resid 723 through 729 removed outlier: 3.553A pdb=" N GLY G 729 " --> pdb=" O PHE G 725 " (cutoff:3.500A) Processing helix chain 'G' and resid 756 through 771 Processing helix chain 'G' and resid 775 through 793 removed outlier: 3.756A pdb=" N ARG G 781 " --> pdb=" O ALA G 777 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL G 786 " --> pdb=" O LYS G 782 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG G 791 " --> pdb=" O ASN G 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 6 Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 25 through 41 removed outlier: 3.566A pdb=" N PHE I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 63 Processing helix chain 'I' and resid 68 through 80 Processing helix chain 'I' and resid 94 through 103 Processing helix chain 'I' and resid 106 through 118 removed outlier: 4.460A pdb=" N ILE I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.605A pdb=" N TRP I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 185 removed outlier: 3.789A pdb=" N SER I 185 " --> pdb=" O LYS I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 196 removed outlier: 3.644A pdb=" N ASP I 196 " --> pdb=" O CYS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 224 removed outlier: 3.512A pdb=" N GLY I 224 " --> pdb=" O ARG I 220 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 233 removed outlier: 4.052A pdb=" N ALA I 232 " --> pdb=" O GLU I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 242 removed outlier: 3.548A pdb=" N LEU I 240 " --> pdb=" O PRO I 237 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN I 242 " --> pdb=" O GLN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 280 Processing helix chain 'I' and resid 285 through 309 Processing helix chain 'I' and resid 331 through 343 Processing helix chain 'I' and resid 362 through 385 Processing helix chain 'I' and resid 396 through 405 removed outlier: 3.557A pdb=" N ASN I 403 " --> pdb=" O GLN I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 456 removed outlier: 3.655A pdb=" N ILE I 448 " --> pdb=" O ASN I 444 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU I 449 " --> pdb=" O GLN I 445 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I 453 " --> pdb=" O LEU I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 462 removed outlier: 3.660A pdb=" N THR I 460 " --> pdb=" O PRO I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 478 No H-bonds generated for 'chain 'I' and resid 476 through 478' Processing helix chain 'I' and resid 479 through 490 removed outlier: 4.380A pdb=" N LEU I 483 " --> pdb=" O LEU I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 505 through 520 Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 537 through 543 Processing helix chain 'I' and resid 553 through 568 removed outlier: 3.521A pdb=" N ARG I 568 " --> pdb=" O TRP I 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 593 Processing helix chain 'I' and resid 599 through 609 removed outlier: 4.241A pdb=" N MET I 609 " --> pdb=" O GLN I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 632 through 647 removed outlier: 4.006A pdb=" N ARG I 641 " --> pdb=" O TYR I 637 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU I 642 " --> pdb=" O GLU I 638 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU I 643 " --> pdb=" O ARG I 639 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL I 644 " --> pdb=" O ALA I 640 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR I 647 " --> pdb=" O LEU I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 649 through 661 removed outlier: 4.015A pdb=" N LEU I 653 " --> pdb=" O MET I 649 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 670 Processing helix chain 'I' and resid 681 through 699 removed outlier: 3.540A pdb=" N LYS I 695 " --> pdb=" O ALA I 691 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA I 697 " --> pdb=" O MET I 693 " (cutoff:3.500A) Processing helix chain 'I' and resid 718 through 721 removed outlier: 3.681A pdb=" N GLU I 721 " --> pdb=" O ASN I 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 718 through 721' Processing helix chain 'I' and resid 722 through 729 removed outlier: 4.338A pdb=" N ARG I 726 " --> pdb=" O HIS I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 771 Processing helix chain 'I' and resid 775 through 793 removed outlier: 3.687A pdb=" N ARG I 781 " --> pdb=" O ALA I 777 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS I 782 " --> pdb=" O ASP I 778 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL I 786 " --> pdb=" O LYS I 782 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG I 791 " --> pdb=" O ASN I 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 8 through 18 Processing helix chain 'J' and resid 25 through 41 Processing helix chain 'J' and resid 45 through 62 Processing helix chain 'J' and resid 68 through 80 Processing helix chain 'J' and resid 94 through 103 removed outlier: 3.640A pdb=" N THR J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 118 Processing helix chain 'J' and resid 120 through 124 removed outlier: 3.520A pdb=" N SER J 123 " --> pdb=" O GLY J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 146 removed outlier: 3.703A pdb=" N TYR J 142 " --> pdb=" O THR J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 171 removed outlier: 4.020A pdb=" N TRP J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 185 removed outlier: 3.544A pdb=" N LEU J 176 " --> pdb=" O PRO J 172 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG J 177 " --> pdb=" O GLU J 173 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 196 removed outlier: 3.789A pdb=" N ILE J 195 " --> pdb=" O LEU J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 224 Processing helix chain 'J' and resid 236 through 241 Processing helix chain 'J' and resid 265 through 280 Processing helix chain 'J' and resid 285 through 310 removed outlier: 3.633A pdb=" N LEU J 291 " --> pdb=" O GLY J 287 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN J 308 " --> pdb=" O THR J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 343 Processing helix chain 'J' and resid 362 through 385 Processing helix chain 'J' and resid 396 through 405 Processing helix chain 'J' and resid 436 through 456 Processing helix chain 'J' and resid 457 through 462 Processing helix chain 'J' and resid 476 through 479 Processing helix chain 'J' and resid 480 through 489 Processing helix chain 'J' and resid 505 through 520 Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 553 through 568 removed outlier: 3.544A pdb=" N ARG J 568 " --> pdb=" O TRP J 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 593 removed outlier: 3.512A pdb=" N ARG J 586 " --> pdb=" O ILE J 582 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 609 removed outlier: 3.609A pdb=" N MET J 609 " --> pdb=" O GLN J 605 " (cutoff:3.500A) Processing helix chain 'J' and resid 610 through 612 No H-bonds generated for 'chain 'J' and resid 610 through 612' Processing helix chain 'J' and resid 615 through 619 Processing helix chain 'J' and resid 632 through 647 removed outlier: 3.718A pdb=" N GLU J 638 " --> pdb=" O LEU J 634 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA J 640 " --> pdb=" O GLU J 636 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG J 641 " --> pdb=" O TYR J 637 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU J 643 " --> pdb=" O ARG J 639 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL J 644 " --> pdb=" O ALA J 640 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR J 647 " --> pdb=" O LEU J 643 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 662 Processing helix chain 'J' and resid 662 through 671 removed outlier: 3.535A pdb=" N GLU J 671 " --> pdb=" O LYS J 667 " (cutoff:3.500A) Processing helix chain 'J' and resid 681 through 699 removed outlier: 3.521A pdb=" N LYS J 695 " --> pdb=" O ALA J 691 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG J 699 " --> pdb=" O LYS J 695 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 721 Processing helix chain 'J' and resid 722 through 729 removed outlier: 4.270A pdb=" N ARG J 726 " --> pdb=" O HIS J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 756 through 771 Processing helix chain 'J' and resid 775 through 793 removed outlier: 3.508A pdb=" N ARG J 781 " --> pdb=" O ALA J 777 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL J 786 " --> pdb=" O LYS J 782 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY J 790 " --> pdb=" O VAL J 786 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG J 791 " --> pdb=" O ASN J 787 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 8 through 18 removed outlier: 3.594A pdb=" N THR K 17 " --> pdb=" O TYR K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 41 Processing helix chain 'K' and resid 45 through 63 Processing helix chain 'K' and resid 68 through 80 removed outlier: 3.712A pdb=" N GLU K 78 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 102 removed outlier: 3.605A pdb=" N THR K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 118 Processing helix chain 'K' and resid 120 through 124 removed outlier: 3.500A pdb=" N SER K 123 " --> pdb=" O GLY K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.769A pdb=" N CYS K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU K 169 " --> pdb=" O TRP K 165 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 184 removed outlier: 3.579A pdb=" N ALA K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 196 Processing helix chain 'K' and resid 200 through 224 Processing helix chain 'K' and resid 229 through 234 removed outlier: 3.814A pdb=" N ALA K 232 " --> pdb=" O GLU K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 242 removed outlier: 4.008A pdb=" N ASN K 242 " --> pdb=" O GLN K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 280 Processing helix chain 'K' and resid 285 through 313 removed outlier: 3.754A pdb=" N TRP K 293 " --> pdb=" O GLU K 289 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP K 311 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE K 312 " --> pdb=" O GLN K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 343 removed outlier: 3.760A pdb=" N LEU K 335 " --> pdb=" O GLU K 331 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY K 343 " --> pdb=" O LYS K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 385 removed outlier: 3.782A pdb=" N ALA K 383 " --> pdb=" O GLU K 379 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS K 384 " --> pdb=" O TYR K 380 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 407 removed outlier: 3.529A pdb=" N ASP K 402 " --> pdb=" O SER K 398 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU K 406 " --> pdb=" O ASP K 402 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL K 407 " --> pdb=" O ASN K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 456 removed outlier: 3.688A pdb=" N ALA K 447 " --> pdb=" O LYS K 443 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N MET K 452 " --> pdb=" O ILE K 448 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU K 453 " --> pdb=" O LEU K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 462 Processing helix chain 'K' and resid 476 through 479 Processing helix chain 'K' and resid 480 through 490 removed outlier: 3.562A pdb=" N LYS K 489 " --> pdb=" O ARG K 485 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER K 490 " --> pdb=" O VAL K 486 " (cutoff:3.500A) Processing helix chain 'K' and resid 505 through 520 removed outlier: 3.540A pdb=" N ARG K 511 " --> pdb=" O ILE K 507 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE K 513 " --> pdb=" O GLY K 509 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 535 Processing helix chain 'K' and resid 537 through 542 Processing helix chain 'K' and resid 553 through 568 removed outlier: 3.556A pdb=" N ARG K 568 " --> pdb=" O TRP K 564 " (cutoff:3.500A) Processing helix chain 'K' and resid 573 through 593 removed outlier: 3.789A pdb=" N ALA K 577 " --> pdb=" O LEU K 573 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 609 Processing helix chain 'K' and resid 610 through 612 No H-bonds generated for 'chain 'K' and resid 610 through 612' Processing helix chain 'K' and resid 615 through 619 removed outlier: 3.800A pdb=" N GLY K 618 " --> pdb=" O GLU K 615 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 647 removed outlier: 3.819A pdb=" N ARG K 641 " --> pdb=" O TYR K 637 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU K 643 " --> pdb=" O ARG K 639 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL K 644 " --> pdb=" O ALA K 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 650 through 662 removed outlier: 3.538A pdb=" N SER K 662 " --> pdb=" O GLN K 658 " (cutoff:3.500A) Processing helix chain 'K' and resid 662 through 671 removed outlier: 3.538A pdb=" N GLU K 671 " --> pdb=" O LYS K 667 " (cutoff:3.500A) Processing helix chain 'K' and resid 681 through 700 Processing helix chain 'K' and resid 718 through 722 Processing helix chain 'K' and resid 723 through 729 removed outlier: 3.652A pdb=" N GLY K 729 " --> pdb=" O PHE K 725 " (cutoff:3.500A) Processing helix chain 'K' and resid 756 through 771 Processing helix chain 'K' and resid 775 through 793 removed outlier: 3.535A pdb=" N VAL K 786 " --> pdb=" O LYS K 782 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY K 790 " --> pdb=" O VAL K 786 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG K 791 " --> pdb=" O ASN K 787 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.565A pdb=" N LEU L 12 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR L 17 " --> pdb=" O TYR L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 41 Processing helix chain 'L' and resid 45 through 63 Processing helix chain 'L' and resid 68 through 80 removed outlier: 3.780A pdb=" N ARG L 74 " --> pdb=" O VAL L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 105 removed outlier: 3.517A pdb=" N THR L 100 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG L 104 " --> pdb=" O THR L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 118 removed outlier: 4.529A pdb=" N ILE L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 124 removed outlier: 3.737A pdb=" N SER L 123 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN L 124 " --> pdb=" O PRO L 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 120 through 124' Processing helix chain 'L' and resid 136 through 146 removed outlier: 3.588A pdb=" N TYR L 142 " --> pdb=" O THR L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 171 removed outlier: 3.715A pdb=" N TRP L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 184 removed outlier: 3.820A pdb=" N ALA L 184 " --> pdb=" O GLU L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 196 Processing helix chain 'L' and resid 200 through 224 removed outlier: 3.669A pdb=" N VAL L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 234 Processing helix chain 'L' and resid 236 through 241 Processing helix chain 'L' and resid 265 through 280 Processing helix chain 'L' and resid 285 through 310 removed outlier: 3.668A pdb=" N GLN L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP L 310 " --> pdb=" O LEU L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 343 removed outlier: 3.848A pdb=" N LEU L 335 " --> pdb=" O GLU L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 385 removed outlier: 3.854A pdb=" N MET L 366 " --> pdb=" O ASP L 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN L 367 " --> pdb=" O PRO L 363 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS L 368 " --> pdb=" O ASN L 364 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA L 383 " --> pdb=" O GLU L 379 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 405 Processing helix chain 'L' and resid 436 through 456 removed outlier: 3.503A pdb=" N ASP L 441 " --> pdb=" O LEU L 437 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE L 448 " --> pdb=" O ASN L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 462 removed outlier: 3.550A pdb=" N GLY L 461 " --> pdb=" O ARG L 458 " (cutoff:3.500A) Processing helix chain 'L' and resid 476 through 478 No H-bonds generated for 'chain 'L' and resid 476 through 478' Processing helix chain 'L' and resid 479 through 490 removed outlier: 4.477A pdb=" N LEU L 483 " --> pdb=" O LEU L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 505 through 520 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 553 through 568 Processing helix chain 'L' and resid 574 through 593 Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 610 through 612 No H-bonds generated for 'chain 'L' and resid 610 through 612' Processing helix chain 'L' and resid 613 through 617 removed outlier: 3.565A pdb=" N GLU L 617 " --> pdb=" O ALA L 614 " (cutoff:3.500A) Processing helix chain 'L' and resid 632 through 647 removed outlier: 3.557A pdb=" N GLU L 636 " --> pdb=" O LEU L 632 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR L 647 " --> pdb=" O LEU L 643 " (cutoff:3.500A) Processing helix chain 'L' and resid 650 through 661 Processing helix chain 'L' and resid 662 through 671 Processing helix chain 'L' and resid 681 through 700 Processing helix chain 'L' and resid 718 through 722 removed outlier: 3.680A pdb=" N GLU L 721 " --> pdb=" O ASN L 718 " (cutoff:3.500A) Processing helix chain 'L' and resid 723 through 729 removed outlier: 3.659A pdb=" N TRP L 727 " --> pdb=" O HIS L 723 " (cutoff:3.500A) Processing helix chain 'L' and resid 756 through 771 Processing helix chain 'L' and resid 775 through 793 removed outlier: 3.578A pdb=" N LYS L 782 " --> pdb=" O ASP L 778 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 791 " --> pdb=" O ASN L 787 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 17 removed outlier: 3.544A pdb=" N THR M 17 " --> pdb=" O TYR M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 41 removed outlier: 3.500A pdb=" N SER M 31 " --> pdb=" O GLU M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 64 Processing helix chain 'M' and resid 68 through 80 removed outlier: 4.066A pdb=" N ARG M 74 " --> pdb=" O VAL M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 103 removed outlier: 3.614A pdb=" N SER M 103 " --> pdb=" O GLN M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 118 Processing helix chain 'M' and resid 120 through 124 removed outlier: 3.601A pdb=" N SER M 123 " --> pdb=" O GLY M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 146 removed outlier: 3.506A pdb=" N ASP M 141 " --> pdb=" O PRO M 137 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR M 142 " --> pdb=" O THR M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 171 removed outlier: 3.902A pdb=" N LEU M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 185 removed outlier: 3.959A pdb=" N SER M 185 " --> pdb=" O LYS M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 196 Processing helix chain 'M' and resid 200 through 224 removed outlier: 3.546A pdb=" N VAL M 221 " --> pdb=" O ILE M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 234 removed outlier: 3.560A pdb=" N ALA M 232 " --> pdb=" O GLU M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 242 removed outlier: 3.716A pdb=" N ASN M 242 " --> pdb=" O GLN M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 279 Processing helix chain 'M' and resid 285 through 311 removed outlier: 3.599A pdb=" N ASP M 311 " --> pdb=" O VAL M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 330 Processing helix chain 'M' and resid 332 through 343 removed outlier: 4.335A pdb=" N SER M 336 " --> pdb=" O LYS M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 385 removed outlier: 3.625A pdb=" N HIS M 384 " --> pdb=" O TYR M 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 396 through 405 Processing helix chain 'M' and resid 436 through 456 Processing helix chain 'M' and resid 457 through 462 Processing helix chain 'M' and resid 476 through 479 Processing helix chain 'M' and resid 480 through 490 Processing helix chain 'M' and resid 505 through 520 Processing helix chain 'M' and resid 531 through 535 Processing helix chain 'M' and resid 537 through 542 Processing helix chain 'M' and resid 553 through 568 Processing helix chain 'M' and resid 573 through 593 removed outlier: 3.701A pdb=" N ALA M 577 " --> pdb=" O LEU M 573 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 609 removed outlier: 3.592A pdb=" N MET M 609 " --> pdb=" O GLN M 605 " (cutoff:3.500A) Processing helix chain 'M' and resid 633 through 646 removed outlier: 3.882A pdb=" N VAL M 644 " --> pdb=" O ALA M 640 " (cutoff:3.500A) Processing helix chain 'M' and resid 650 through 662 removed outlier: 3.600A pdb=" N GLN M 658 " --> pdb=" O LYS M 654 " (cutoff:3.500A) Processing helix chain 'M' and resid 662 through 671 Processing helix chain 'M' and resid 681 through 700 removed outlier: 3.691A pdb=" N VAL M 686 " --> pdb=" O ASP M 682 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU M 688 " --> pdb=" O ALA M 684 " (cutoff:3.500A) Processing helix chain 'M' and resid 718 through 722 removed outlier: 3.796A pdb=" N GLU M 721 " --> pdb=" O ASN M 718 " (cutoff:3.500A) Processing helix chain 'M' and resid 723 through 729 Processing helix chain 'M' and resid 756 through 771 Processing helix chain 'M' and resid 775 through 793 removed outlier: 3.683A pdb=" N ARG M 781 " --> pdb=" O ALA M 777 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS M 782 " --> pdb=" O ASP M 778 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL M 786 " --> pdb=" O LYS M 782 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG M 791 " --> pdb=" O ASN M 787 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 8 through 17 Processing helix chain 'N' and resid 25 through 41 removed outlier: 3.700A pdb=" N GLU N 39 " --> pdb=" O LEU N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 63 Processing helix chain 'N' and resid 68 through 80 removed outlier: 3.809A pdb=" N ARG N 74 " --> pdb=" O VAL N 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU N 75 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 103 Processing helix chain 'N' and resid 107 through 118 Processing helix chain 'N' and resid 120 through 124 removed outlier: 3.561A pdb=" N SER N 123 " --> pdb=" O GLY N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 146 removed outlier: 3.940A pdb=" N TYR N 142 " --> pdb=" O THR N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 171 removed outlier: 3.770A pdb=" N CYS N 164 " --> pdb=" O SER N 160 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 184 Processing helix chain 'N' and resid 185 through 196 removed outlier: 3.550A pdb=" N LYS N 189 " --> pdb=" O SER N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 224 Processing helix chain 'N' and resid 236 through 243 removed outlier: 3.606A pdb=" N ASN N 242 " --> pdb=" O GLN N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 280 Processing helix chain 'N' and resid 285 through 310 removed outlier: 4.405A pdb=" N LEU N 291 " --> pdb=" O GLY N 287 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP N 310 " --> pdb=" O LEU N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 343 removed outlier: 3.946A pdb=" N LEU N 335 " --> pdb=" O GLU N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 385 removed outlier: 3.819A pdb=" N ALA N 383 " --> pdb=" O GLU N 379 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS N 384 " --> pdb=" O TYR N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 405 Processing helix chain 'N' and resid 436 through 456 removed outlier: 3.540A pdb=" N ILE N 448 " --> pdb=" O ASN N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 457 through 462 Processing helix chain 'N' and resid 476 through 479 Processing helix chain 'N' and resid 480 through 489 removed outlier: 3.500A pdb=" N LYS N 489 " --> pdb=" O ARG N 485 " (cutoff:3.500A) Processing helix chain 'N' and resid 505 through 520 Processing helix chain 'N' and resid 531 through 535 Processing helix chain 'N' and resid 537 through 542 Processing helix chain 'N' and resid 553 through 568 Processing helix chain 'N' and resid 571 through 573 No H-bonds generated for 'chain 'N' and resid 571 through 573' Processing helix chain 'N' and resid 574 through 593 removed outlier: 3.541A pdb=" N LYS N 590 " --> pdb=" O ARG N 586 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 609 removed outlier: 3.587A pdb=" N MET N 609 " --> pdb=" O GLN N 605 " (cutoff:3.500A) Processing helix chain 'N' and resid 610 through 612 No H-bonds generated for 'chain 'N' and resid 610 through 612' Processing helix chain 'N' and resid 613 through 619 removed outlier: 3.644A pdb=" N GLY N 618 " --> pdb=" O ALA N 614 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU N 619 " --> pdb=" O GLU N 615 " (cutoff:3.500A) Processing helix chain 'N' and resid 632 through 645 removed outlier: 3.685A pdb=" N ALA N 640 " --> pdb=" O GLU N 636 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU N 643 " --> pdb=" O ARG N 639 " (cutoff:3.500A) Processing helix chain 'N' and resid 649 through 661 Processing helix chain 'N' and resid 662 through 671 Processing helix chain 'N' and resid 681 through 699 Processing helix chain 'N' and resid 718 through 722 Processing helix chain 'N' and resid 723 through 729 Processing helix chain 'N' and resid 756 through 772 Processing helix chain 'N' and resid 775 through 793 removed outlier: 3.522A pdb=" N VAL N 786 " --> pdb=" O LYS N 782 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY N 790 " --> pdb=" O VAL N 786 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG N 791 " --> pdb=" O ASN N 787 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 51 removed outlier: 3.964A pdb=" N ASP O 39 " --> pdb=" O LYS O 35 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL O 42 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU O 43 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER O 44 " --> pdb=" O GLN O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 95 removed outlier: 3.547A pdb=" N PHE O 85 " --> pdb=" O GLY O 81 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE O 86 " --> pdb=" O LYS O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 137 removed outlier: 3.781A pdb=" N MET O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 168 removed outlier: 4.002A pdb=" N LYS O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS O 165 " --> pdb=" O GLN O 161 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU O 166 " --> pdb=" O ARG O 162 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU O 167 " --> pdb=" O GLY O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 182 removed outlier: 3.799A pdb=" N PHE O 177 " --> pdb=" O LYS O 173 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER O 178 " --> pdb=" O PRO O 174 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP O 179 " --> pdb=" O GLU O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 211 removed outlier: 4.042A pdb=" N ILE O 199 " --> pdb=" O ASP O 195 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU O 201 " --> pdb=" O SER O 197 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU O 202 " --> pdb=" O GLU O 198 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU O 203 " --> pdb=" O ILE O 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 240 removed outlier: 3.521A pdb=" N VAL O 233 " --> pdb=" O ALA O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 268 removed outlier: 3.611A pdb=" N TYR O 257 " --> pdb=" O ASP O 253 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN O 268 " --> pdb=" O LYS O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 277 Processing helix chain 'O' and resid 279 through 302 Processing helix chain 'O' and resid 312 through 318 Processing helix chain 'O' and resid 344 through 356 removed outlier: 3.838A pdb=" N GLU O 354 " --> pdb=" O ASP O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 361 through 373 removed outlier: 3.738A pdb=" N VAL O 368 " --> pdb=" O ALA O 364 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN O 369 " --> pdb=" O ASP O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 395 removed outlier: 3.550A pdb=" N SER O 395 " --> pdb=" O TYR O 391 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 425 removed outlier: 3.510A pdb=" N LEU O 416 " --> pdb=" O SER O 412 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY O 423 " --> pdb=" O ASN O 419 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER O 424 " --> pdb=" O ALA O 420 " (cutoff:3.500A) Processing helix chain 'O' and resid 426 through 433 removed outlier: 4.242A pdb=" N TYR O 430 " --> pdb=" O LEU O 426 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG O 431 " --> pdb=" O SER O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 442 through 458 Processing helix chain 'O' and resid 472 through 490 removed outlier: 3.812A pdb=" N ILE O 480 " --> pdb=" O ARG O 476 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR O 481 " --> pdb=" O ASN O 477 " (cutoff:3.500A) Processing helix chain 'O' and resid 494 through 503 Processing helix chain 'O' and resid 505 through 514 removed outlier: 3.626A pdb=" N SER O 509 " --> pdb=" O CYS O 505 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN O 512 " --> pdb=" O VAL O 508 " (cutoff:3.500A) Processing helix chain 'O' and resid 525 through 538 removed outlier: 4.032A pdb=" N GLU O 529 " --> pdb=" O ARG O 525 " (cutoff:3.500A) Processing helix chain 'O' and resid 546 through 560 Processing helix chain 'O' and resid 563 through 567 removed outlier: 3.551A pdb=" N ILE O 567 " --> pdb=" O ASP O 564 " (cutoff:3.500A) Processing helix chain 'O' and resid 597 through 606 Processing helix chain 'O' and resid 622 through 636 removed outlier: 3.586A pdb=" N ILE O 632 " --> pdb=" O ALA O 628 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER O 633 " --> pdb=" O ILE O 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA O 634 " --> pdb=" O ALA O 630 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS O 635 " --> pdb=" O ASP O 631 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG O 636 " --> pdb=" O ILE O 632 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 646 removed outlier: 3.639A pdb=" N PHE O 646 " --> pdb=" O ILE O 642 " (cutoff:3.500A) Processing helix chain 'O' and resid 701 through 716 removed outlier: 3.687A pdb=" N GLU O 705 " --> pdb=" O ASP O 701 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP O 708 " --> pdb=" O THR O 704 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA O 709 " --> pdb=" O GLU O 705 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU O 714 " --> pdb=" O ILE O 710 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP O 716 " --> pdb=" O LYS O 712 " (cutoff:3.500A) Processing helix chain 'O' and resid 719 through 724 removed outlier: 3.508A pdb=" N ILE O 723 " --> pdb=" O ASN O 719 " (cutoff:3.500A) Processing helix chain 'O' and resid 725 through 727 No H-bonds generated for 'chain 'O' and resid 725 through 727' Processing helix chain 'O' and resid 730 through 746 removed outlier: 3.913A pdb=" N ASN O 746 " --> pdb=" O TYR O 742 " (cutoff:3.500A) Processing helix chain 'O' and resid 746 through 751 removed outlier: 4.217A pdb=" N ASP O 750 " --> pdb=" O ASN O 746 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN O 751 " --> pdb=" O ASN O 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 746 through 751' Processing helix chain 'O' and resid 770 through 786 removed outlier: 4.673A pdb=" N VAL O 786 " --> pdb=" O PHE O 782 " (cutoff:3.500A) Processing helix chain 'O' and resid 786 through 791 removed outlier: 4.028A pdb=" N SER O 791 " --> pdb=" O LEU O 787 " (cutoff:3.500A) Processing helix chain 'O' and resid 814 through 830 removed outlier: 3.536A pdb=" N LYS O 819 " --> pdb=" O ASP O 815 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA O 830 " --> pdb=" O GLU O 826 " (cutoff:3.500A) Processing helix chain 'O' and resid 834 through 839 removed outlier: 3.769A pdb=" N HIS O 839 " --> pdb=" O TRP O 835 " (cutoff:3.500A) Processing helix chain 'O' and resid 839 through 846 removed outlier: 3.533A pdb=" N ILE O 846 " --> pdb=" O PHE O 842 " (cutoff:3.500A) Processing helix chain 'O' and resid 867 through 883 removed outlier: 3.793A pdb=" N SER O 873 " --> pdb=" O ASN O 869 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY O 883 " --> pdb=" O ASP O 879 " (cutoff:3.500A) Processing helix chain 'O' and resid 890 through 898 removed outlier: 3.856A pdb=" N TYR O 894 " --> pdb=" O GLU O 890 " (cutoff:3.500A) Processing helix chain 'O' and resid 915 through 919 removed outlier: 4.132A pdb=" N ASN O 918 " --> pdb=" O THR O 915 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 27 removed outlier: 3.864A pdb=" N THR P 27 " --> pdb=" O PRO P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 49 Processing helix chain 'P' and resid 82 through 94 Processing helix chain 'P' and resid 111 through 115 Processing helix chain 'P' and resid 121 through 141 removed outlier: 3.679A pdb=" N MET P 132 " --> pdb=" O ARG P 128 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS P 136 " --> pdb=" O MET P 132 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 169 removed outlier: 3.503A pdb=" N LYS P 148 " --> pdb=" O ASN P 144 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN P 159 " --> pdb=" O ASN P 155 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG P 162 " --> pdb=" O ALA P 158 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY P 163 " --> pdb=" O GLN P 159 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU P 166 " --> pdb=" O ARG P 162 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU P 167 " --> pdb=" O GLY P 163 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP P 169 " --> pdb=" O HIS P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 181 removed outlier: 3.856A pdb=" N SER P 178 " --> pdb=" O PRO P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 189 removed outlier: 3.771A pdb=" N ASP P 188 " --> pdb=" O ALA P 185 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR P 189 " --> pdb=" O GLN P 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 185 through 189' Processing helix chain 'P' and resid 195 through 212 removed outlier: 3.894A pdb=" N ILE P 199 " --> pdb=" O ASP P 195 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU P 201 " --> pdb=" O SER P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 240 removed outlier: 4.238A pdb=" N VAL P 233 " --> pdb=" O ALA P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 268 removed outlier: 3.611A pdb=" N TYR P 257 " --> pdb=" O ASP P 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 267 " --> pdb=" O GLY P 263 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN P 268 " --> pdb=" O LYS P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 277 Processing helix chain 'P' and resid 279 through 302 removed outlier: 3.741A pdb=" N GLU P 291 " --> pdb=" O GLY P 287 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 305 No H-bonds generated for 'chain 'P' and resid 303 through 305' Processing helix chain 'P' and resid 312 through 318 Processing helix chain 'P' and resid 343 through 357 Processing helix chain 'P' and resid 361 through 373 Processing helix chain 'P' and resid 375 through 395 Processing helix chain 'P' and resid 412 through 425 removed outlier: 3.869A pdb=" N ALA P 420 " --> pdb=" O LEU P 416 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY P 423 " --> pdb=" O ASN P 419 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET P 425 " --> pdb=" O LEU P 421 " (cutoff:3.500A) Processing helix chain 'P' and resid 427 through 431 Processing helix chain 'P' and resid 442 through 458 removed outlier: 4.190A pdb=" N CYS P 447 " --> pdb=" O MET P 443 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS P 448 " --> pdb=" O ASP P 444 " (cutoff:3.500A) Processing helix chain 'P' and resid 462 through 466 removed outlier: 3.543A pdb=" N TYR P 465 " --> pdb=" O THR P 462 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU P 466 " --> pdb=" O GLY P 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 462 through 466' Processing helix chain 'P' and resid 473 through 490 removed outlier: 3.608A pdb=" N CYS P 478 " --> pdb=" O ALA P 474 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER P 479 " --> pdb=" O LEU P 475 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN P 485 " --> pdb=" O TYR P 481 " (cutoff:3.500A) Processing helix chain 'P' and resid 493 through 514 removed outlier: 3.742A pdb=" N PHE P 497 " --> pdb=" O SER P 493 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN P 499 " --> pdb=" O SER P 495 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU P 502 " --> pdb=" O LEU P 498 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS P 505 " --> pdb=" O LEU P 501 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER P 507 " --> pdb=" O VAL P 503 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL P 508 " --> pdb=" O GLY P 504 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER P 509 " --> pdb=" O CYS P 505 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN P 513 " --> pdb=" O SER P 509 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE P 514 " --> pdb=" O ILE P 510 " (cutoff:3.500A) Processing helix chain 'P' and resid 525 through 539 removed outlier: 3.882A pdb=" N GLU P 529 " --> pdb=" O ARG P 525 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA P 537 " --> pdb=" O SER P 533 " (cutoff:3.500A) Processing helix chain 'P' and resid 546 through 558 removed outlier: 3.502A pdb=" N ASN P 552 " --> pdb=" O SER P 548 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG P 553 " --> pdb=" O HIS P 549 " (cutoff:3.500A) Processing helix chain 'P' and resid 563 through 567 removed outlier: 3.884A pdb=" N LYS P 566 " --> pdb=" O ASN P 563 " (cutoff:3.500A) Processing helix chain 'P' and resid 592 through 596 removed outlier: 3.937A pdb=" N THR P 595 " --> pdb=" O ASN P 592 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU P 596 " --> pdb=" O ILE P 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 592 through 596' Processing helix chain 'P' and resid 597 through 608 Processing helix chain 'P' and resid 621 through 636 removed outlier: 4.279A pdb=" N LEU P 625 " --> pdb=" O SER P 621 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER P 633 " --> pdb=" O ILE P 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS P 635 " --> pdb=" O ASP P 631 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG P 636 " --> pdb=" O ILE P 632 " (cutoff:3.500A) Processing helix chain 'P' and resid 642 through 646 removed outlier: 4.243A pdb=" N PHE P 646 " --> pdb=" O THR P 643 " (cutoff:3.500A) Processing helix chain 'P' and resid 701 through 721 removed outlier: 4.132A pdb=" N GLU P 705 " --> pdb=" O ASP P 701 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE P 706 " --> pdb=" O ASP P 702 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER P 707 " --> pdb=" O ALA P 703 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN P 719 " --> pdb=" O GLN P 715 " (cutoff:3.500A) Processing helix chain 'P' and resid 723 through 727 removed outlier: 3.620A pdb=" N ILE P 727 " --> pdb=" O GLU P 724 " (cutoff:3.500A) Processing helix chain 'P' and resid 730 through 752 removed outlier: 3.629A pdb=" N ARG P 740 " --> pdb=" O LYS P 736 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN P 746 " --> pdb=" O TYR P 742 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN P 747 " --> pdb=" O PHE P 743 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL P 748 " --> pdb=" O ASN P 744 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA P 749 " --> pdb=" O LEU P 745 " (cutoff:3.500A) Processing helix chain 'P' and resid 770 through 789 removed outlier: 3.774A pdb=" N VAL P 779 " --> pdb=" O MET P 775 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL P 786 " --> pdb=" O PHE P 782 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU P 787 " --> pdb=" O LEU P 783 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL P 788 " --> pdb=" O HIS P 784 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU P 789 " --> pdb=" O ALA P 785 " (cutoff:3.500A) Processing helix chain 'P' and resid 814 through 831 removed outlier: 3.685A pdb=" N LYS P 827 " --> pdb=" O ILE P 823 " (cutoff:3.500A) Processing helix chain 'P' and resid 834 through 839 removed outlier: 3.610A pdb=" N THR P 838 " --> pdb=" O THR P 834 " (cutoff:3.500A) Processing helix chain 'P' and resid 841 through 846 Processing helix chain 'P' and resid 857 through 861 removed outlier: 3.874A pdb=" N ILE P 861 " --> pdb=" O VAL P 858 " (cutoff:3.500A) Processing helix chain 'P' and resid 866 through 883 removed outlier: 3.868A pdb=" N LYS P 870 " --> pdb=" O LYS P 866 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE P 878 " --> pdb=" O PHE P 874 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP P 879 " --> pdb=" O ASN P 875 " (cutoff:3.500A) Processing helix chain 'P' and resid 888 through 898 removed outlier: 3.776A pdb=" N ASN P 898 " --> pdb=" O TYR P 894 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 51 removed outlier: 3.718A pdb=" N ARG Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP Q 39 " --> pdb=" O LYS Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 95 removed outlier: 3.511A pdb=" N ASN Q 87 " --> pdb=" O THR Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 115 Processing helix chain 'Q' and resid 121 through 141 Processing helix chain 'Q' and resid 145 through 169 removed outlier: 3.631A pdb=" N GLN Q 149 " --> pdb=" O ASP Q 145 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN Q 152 " --> pdb=" O LYS Q 148 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N HIS Q 165 " --> pdb=" O GLN Q 161 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU Q 166 " --> pdb=" O ARG Q 162 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU Q 167 " --> pdb=" O GLY Q 163 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP Q 169 " --> pdb=" O HIS Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 180 removed outlier: 3.614A pdb=" N PHE Q 177 " --> pdb=" O LYS Q 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER Q 178 " --> pdb=" O PRO Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 211 Processing helix chain 'Q' and resid 229 through 241 Processing helix chain 'Q' and resid 253 through 267 removed outlier: 3.850A pdb=" N TYR Q 257 " --> pdb=" O ASP Q 253 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU Q 267 " --> pdb=" O GLY Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 277 removed outlier: 4.342A pdb=" N GLU Q 275 " --> pdb=" O LYS Q 271 " (cutoff:3.500A) Processing helix chain 'Q' and resid 279 through 300 removed outlier: 3.577A pdb=" N LEU Q 293 " --> pdb=" O MET Q 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN Q 295 " --> pdb=" O GLU Q 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 312 through 318 Processing helix chain 'Q' and resid 343 through 356 removed outlier: 3.541A pdb=" N GLU Q 354 " --> pdb=" O ASP Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 361 through 373 removed outlier: 3.588A pdb=" N TYR Q 367 " --> pdb=" O ASP Q 363 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Q 368 " --> pdb=" O ALA Q 364 " (cutoff:3.500A) Processing helix chain 'Q' and resid 375 through 394 removed outlier: 3.534A pdb=" N LEU Q 383 " --> pdb=" O LEU Q 379 " (cutoff:3.500A) Processing helix chain 'Q' and resid 412 through 425 removed outlier: 3.934A pdb=" N ALA Q 420 " --> pdb=" O LEU Q 416 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY Q 423 " --> pdb=" O ASN Q 419 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 433 Processing helix chain 'Q' and resid 442 through 458 removed outlier: 3.547A pdb=" N LYS Q 448 " --> pdb=" O ASP Q 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE Q 451 " --> pdb=" O CYS Q 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP Q 457 " --> pdb=" O TYR Q 453 " (cutoff:3.500A) Processing helix chain 'Q' and resid 462 through 466 Processing helix chain 'Q' and resid 472 through 490 removed outlier: 4.252A pdb=" N SER Q 479 " --> pdb=" O LEU Q 475 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE Q 480 " --> pdb=" O ARG Q 476 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR Q 481 " --> pdb=" O ASN Q 477 " (cutoff:3.500A) Processing helix chain 'Q' and resid 493 through 515 removed outlier: 3.586A pdb=" N GLN Q 499 " --> pdb=" O SER Q 495 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL Q 508 " --> pdb=" O GLY Q 504 " (cutoff:3.500A) Processing helix chain 'Q' and resid 525 through 540 removed outlier: 3.672A pdb=" N SER Q 540 " --> pdb=" O VAL Q 536 " (cutoff:3.500A) Processing helix chain 'Q' and resid 546 through 559 removed outlier: 4.154A pdb=" N ARG Q 553 " --> pdb=" O HIS Q 549 " (cutoff:3.500A) Processing helix chain 'Q' and resid 563 through 567 Processing helix chain 'Q' and resid 592 through 596 removed outlier: 3.991A pdb=" N THR Q 595 " --> pdb=" O ASN Q 592 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU Q 596 " --> pdb=" O ILE Q 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 592 through 596' Processing helix chain 'Q' and resid 597 through 606 Processing helix chain 'Q' and resid 622 through 636 removed outlier: 3.506A pdb=" N SER Q 633 " --> pdb=" O ILE Q 629 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG Q 636 " --> pdb=" O ILE Q 632 " (cutoff:3.500A) Processing helix chain 'Q' and resid 639 through 645 Processing helix chain 'Q' and resid 701 through 718 removed outlier: 3.754A pdb=" N GLU Q 705 " --> pdb=" O ASP Q 701 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE Q 706 " --> pdb=" O ASP Q 702 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER Q 707 " --> pdb=" O ALA Q 703 " (cutoff:3.500A) Processing helix chain 'Q' and resid 720 through 725 removed outlier: 3.729A pdb=" N ILE Q 725 " --> pdb=" O ASN Q 721 " (cutoff:3.500A) Processing helix chain 'Q' and resid 730 through 752 removed outlier: 3.816A pdb=" N TRP Q 738 " --> pdb=" O ILE Q 734 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE Q 743 " --> pdb=" O SER Q 739 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN Q 747 " --> pdb=" O PHE Q 743 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL Q 748 " --> pdb=" O ASN Q 744 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS Q 752 " --> pdb=" O VAL Q 748 " (cutoff:3.500A) Processing helix chain 'Q' and resid 770 through 791 removed outlier: 3.964A pdb=" N GLU Q 789 " --> pdb=" O ALA Q 785 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER Q 791 " --> pdb=" O LEU Q 787 " (cutoff:3.500A) Processing helix chain 'Q' and resid 814 through 831 Processing helix chain 'Q' and resid 834 through 839 Processing helix chain 'Q' and resid 839 through 846 removed outlier: 3.943A pdb=" N PHE Q 843 " --> pdb=" O HIS Q 839 " (cutoff:3.500A) Processing helix chain 'Q' and resid 851 through 856 Processing helix chain 'Q' and resid 866 through 883 removed outlier: 4.012A pdb=" N LYS Q 870 " --> pdb=" O LYS Q 866 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER Q 873 " --> pdb=" O ASN Q 869 " (cutoff:3.500A) Processing helix chain 'Q' and resid 888 through 898 Processing helix chain 'R' and resid 34 through 51 removed outlier: 3.501A pdb=" N ASP R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR R 51 " --> pdb=" O ASN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 94 removed outlier: 3.758A pdb=" N SER R 92 " --> pdb=" O SER R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 140 removed outlier: 3.578A pdb=" N THR R 124 " --> pdb=" O PRO R 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET R 132 " --> pdb=" O ARG R 128 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL R 133 " --> pdb=" O LEU R 129 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR R 140 " --> pdb=" O LYS R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 165 removed outlier: 4.047A pdb=" N ARG R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS R 148 " --> pdb=" O ASN R 144 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY R 163 " --> pdb=" O GLN R 159 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 180 Processing helix chain 'R' and resid 196 through 211 Processing helix chain 'R' and resid 229 through 241 Processing helix chain 'R' and resid 253 through 267 removed outlier: 3.823A pdb=" N TYR R 266 " --> pdb=" O ARG R 262 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU R 267 " --> pdb=" O GLY R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 277 removed outlier: 3.581A pdb=" N GLU R 277 " --> pdb=" O LEU R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 302 removed outlier: 3.616A pdb=" N GLU R 291 " --> pdb=" O GLY R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 307 Processing helix chain 'R' and resid 312 through 318 Processing helix chain 'R' and resid 344 through 354 removed outlier: 4.306A pdb=" N GLU R 354 " --> pdb=" O ASP R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 374 removed outlier: 3.750A pdb=" N TYR R 367 " --> pdb=" O ASP R 363 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 368 " --> pdb=" O ALA R 364 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN R 374 " --> pdb=" O GLU R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 395 removed outlier: 3.883A pdb=" N HIS R 392 " --> pdb=" O THR R 388 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA R 393 " --> pdb=" O LYS R 389 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR R 394 " --> pdb=" O LYS R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 412 through 425 removed outlier: 3.974A pdb=" N GLY R 423 " --> pdb=" O ASN R 419 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER R 424 " --> pdb=" O ALA R 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 425 through 433 removed outlier: 4.412A pdb=" N ARG R 431 " --> pdb=" O SER R 427 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA R 432 " --> pdb=" O SER R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 443 through 456 removed outlier: 3.621A pdb=" N GLN R 456 " --> pdb=" O THR R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 462 through 466 Processing helix chain 'R' and resid 472 through 490 removed outlier: 4.533A pdb=" N ILE R 480 " --> pdb=" O ARG R 476 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR R 481 " --> pdb=" O ASN R 477 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS R 490 " --> pdb=" O VAL R 486 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 503 Processing helix chain 'R' and resid 506 through 515 Processing helix chain 'R' and resid 525 through 539 removed outlier: 4.000A pdb=" N GLU R 529 " --> pdb=" O ARG R 525 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 537 " --> pdb=" O SER R 533 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET R 539 " --> pdb=" O TYR R 535 " (cutoff:3.500A) Processing helix chain 'R' and resid 546 through 560 removed outlier: 3.887A pdb=" N TRP R 550 " --> pdb=" O SER R 546 " (cutoff:3.500A) Processing helix chain 'R' and resid 563 through 567 Processing helix chain 'R' and resid 597 through 608 removed outlier: 3.745A pdb=" N ALA R 603 " --> pdb=" O LEU R 599 " (cutoff:3.500A) Processing helix chain 'R' and resid 622 through 636 removed outlier: 3.525A pdb=" N ILE R 632 " --> pdb=" O ALA R 628 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER R 633 " --> pdb=" O ILE R 629 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG R 636 " --> pdb=" O ILE R 632 " (cutoff:3.500A) Processing helix chain 'R' and resid 701 through 723 removed outlier: 3.511A pdb=" N PHE R 706 " --> pdb=" O ASP R 702 " (cutoff:3.500A) Processing helix chain 'R' and resid 730 through 750 removed outlier: 3.645A pdb=" N ASN R 746 " --> pdb=" O TYR R 742 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN R 747 " --> pdb=" O PHE R 743 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP R 750 " --> pdb=" O ASN R 746 " (cutoff:3.500A) Processing helix chain 'R' and resid 770 through 791 removed outlier: 4.237A pdb=" N PHE R 782 " --> pdb=" O ASN R 778 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU R 789 " --> pdb=" O ALA R 785 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER R 791 " --> pdb=" O LEU R 787 " (cutoff:3.500A) Processing helix chain 'R' and resid 814 through 829 Processing helix chain 'R' and resid 834 through 839 Processing helix chain 'R' and resid 839 through 846 removed outlier: 3.821A pdb=" N ILE R 846 " --> pdb=" O PHE R 842 " (cutoff:3.500A) Processing helix chain 'R' and resid 848 through 852 removed outlier: 3.515A pdb=" N LEU R 851 " --> pdb=" O CYS R 848 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS R 852 " --> pdb=" O PRO R 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 848 through 852' Processing helix chain 'R' and resid 866 through 883 removed outlier: 4.065A pdb=" N LYS R 870 " --> pdb=" O LYS R 866 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER R 873 " --> pdb=" O ASN R 869 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY R 883 " --> pdb=" O ASP R 879 " (cutoff:3.500A) Processing helix chain 'R' and resid 888 through 898 Processing helix chain 'S' and resid 35 through 49 removed outlier: 3.979A pdb=" N GLU S 43 " --> pdb=" O ASP S 39 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER S 44 " --> pdb=" O GLN S 40 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE S 45 " --> pdb=" O LEU S 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE S 49 " --> pdb=" O ILE S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 95 removed outlier: 3.991A pdb=" N ILE S 86 " --> pdb=" O LYS S 82 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN S 87 " --> pdb=" O THR S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 141 removed outlier: 3.660A pdb=" N THR S 124 " --> pdb=" O PRO S 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET S 132 " --> pdb=" O ARG S 128 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL S 133 " --> pdb=" O LEU S 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 162 Processing helix chain 'S' and resid 163 through 169 removed outlier: 4.033A pdb=" N LEU S 167 " --> pdb=" O GLY S 163 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR S 168 " --> pdb=" O LEU S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 180 removed outlier: 4.407A pdb=" N SER S 178 " --> pdb=" O PRO S 174 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP S 179 " --> pdb=" O GLU S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 189 removed outlier: 4.031A pdb=" N ASP S 188 " --> pdb=" O ALA S 185 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 189 " --> pdb=" O GLN S 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 185 through 189' Processing helix chain 'S' and resid 195 through 211 removed outlier: 3.736A pdb=" N ILE S 199 " --> pdb=" O ASP S 195 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU S 202 " --> pdb=" O GLU S 198 " (cutoff:3.500A) Processing helix chain 'S' and resid 230 through 240 removed outlier: 3.749A pdb=" N LEU S 234 " --> pdb=" O GLY S 230 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU S 235 " --> pdb=" O TRP S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 253 through 269 removed outlier: 3.603A pdb=" N TYR S 266 " --> pdb=" O ARG S 262 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU S 267 " --> pdb=" O GLY S 263 " (cutoff:3.500A) Processing helix chain 'S' and resid 271 through 277 removed outlier: 4.300A pdb=" N GLU S 275 " --> pdb=" O LYS S 271 " (cutoff:3.500A) Processing helix chain 'S' and resid 279 through 302 removed outlier: 3.587A pdb=" N GLU S 285 " --> pdb=" O VAL S 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG S 286 " --> pdb=" O ARG S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 312 through 318 Processing helix chain 'S' and resid 343 through 357 Processing helix chain 'S' and resid 361 through 373 removed outlier: 3.570A pdb=" N LEU S 372 " --> pdb=" O VAL S 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 375 through 395 removed outlier: 3.533A pdb=" N LEU S 383 " --> pdb=" O LEU S 379 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR S 394 " --> pdb=" O LYS S 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 412 through 423 removed outlier: 4.104A pdb=" N GLY S 423 " --> pdb=" O ASN S 419 " (cutoff:3.500A) Processing helix chain 'S' and resid 425 through 433 removed outlier: 3.976A pdb=" N ILE S 429 " --> pdb=" O MET S 425 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR S 430 " --> pdb=" O LEU S 426 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG S 431 " --> pdb=" O SER S 427 " (cutoff:3.500A) Processing helix chain 'S' and resid 443 through 458 removed outlier: 3.502A pdb=" N CYS S 447 " --> pdb=" O MET S 443 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS S 455 " --> pdb=" O PHE S 451 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN S 456 " --> pdb=" O THR S 452 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP S 457 " --> pdb=" O TYR S 453 " (cutoff:3.500A) Processing helix chain 'S' and resid 473 through 490 removed outlier: 4.092A pdb=" N SER S 479 " --> pdb=" O LEU S 475 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE S 480 " --> pdb=" O ARG S 476 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR S 481 " --> pdb=" O ASN S 477 " (cutoff:3.500A) Processing helix chain 'S' and resid 494 through 503 Processing helix chain 'S' and resid 505 through 515 removed outlier: 4.409A pdb=" N SER S 509 " --> pdb=" O CYS S 505 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE S 510 " --> pdb=" O GLY S 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 525 through 539 removed outlier: 3.892A pdb=" N GLU S 529 " --> pdb=" O ARG S 525 " (cutoff:3.500A) Processing helix chain 'S' and resid 546 through 561 removed outlier: 3.821A pdb=" N TRP S 550 " --> pdb=" O SER S 546 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA S 551 " --> pdb=" O ALA S 547 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER S 561 " --> pdb=" O VAL S 557 " (cutoff:3.500A) Processing helix chain 'S' and resid 563 through 567 Processing helix chain 'S' and resid 597 through 606 removed outlier: 3.950A pdb=" N MET S 604 " --> pdb=" O ALA S 600 " (cutoff:3.500A) Processing helix chain 'S' and resid 622 through 631 removed outlier: 3.753A pdb=" N ILE S 629 " --> pdb=" O LEU S 625 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA S 630 " --> pdb=" O ILE S 626 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP S 631 " --> pdb=" O GLY S 627 " (cutoff:3.500A) Processing helix chain 'S' and resid 631 through 636 removed outlier: 4.394A pdb=" N CYS S 635 " --> pdb=" O ASP S 631 " (cutoff:3.500A) Processing helix chain 'S' and resid 705 through 717 removed outlier: 4.004A pdb=" N ALA S 709 " --> pdb=" O GLU S 705 " (cutoff:3.500A) Processing helix chain 'S' and resid 718 through 720 No H-bonds generated for 'chain 'S' and resid 718 through 720' Processing helix chain 'S' and resid 722 through 727 removed outlier: 3.835A pdb=" N ILE S 725 " --> pdb=" O GLU S 722 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE S 727 " --> pdb=" O GLU S 724 " (cutoff:3.500A) Processing helix chain 'S' and resid 730 through 752 removed outlier: 4.970A pdb=" N TRP S 738 " --> pdb=" O ILE S 734 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER S 739 " --> pdb=" O GLY S 735 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN S 746 " --> pdb=" O TYR S 742 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN S 747 " --> pdb=" O PHE S 743 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL S 748 " --> pdb=" O ASN S 744 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA S 749 " --> pdb=" O LEU S 745 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP S 750 " --> pdb=" O ASN S 746 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN S 751 " --> pdb=" O ASN S 747 " (cutoff:3.500A) Processing helix chain 'S' and resid 753 through 756 removed outlier: 4.015A pdb=" N LEU S 756 " --> pdb=" O LYS S 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 753 through 756' Processing helix chain 'S' and resid 770 through 793 removed outlier: 3.525A pdb=" N VAL S 788 " --> pdb=" O HIS S 784 " (cutoff:3.500A) Processing helix chain 'S' and resid 814 through 831 removed outlier: 3.841A pdb=" N GLU S 826 " --> pdb=" O LYS S 822 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS S 827 " --> pdb=" O ILE S 823 " (cutoff:3.500A) Processing helix chain 'S' and resid 834 through 839 Processing helix chain 'S' and resid 839 through 847 removed outlier: 3.831A pdb=" N SER S 847 " --> pdb=" O PHE S 843 " (cutoff:3.500A) Processing helix chain 'S' and resid 851 through 856 removed outlier: 4.146A pdb=" N PHE S 856 " --> pdb=" O HIS S 852 " (cutoff:3.500A) Processing helix chain 'S' and resid 867 through 883 removed outlier: 4.680A pdb=" N SER S 873 " --> pdb=" O ASN S 869 " (cutoff:3.500A) Processing helix chain 'S' and resid 888 through 898 Processing helix chain 'T' and resid 35 through 49 removed outlier: 3.544A pdb=" N ASP T 39 " --> pdb=" O LYS T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 95 removed outlier: 3.518A pdb=" N PHE T 85 " --> pdb=" O GLY T 81 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE T 86 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER T 95 " --> pdb=" O LYS T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 115 Processing helix chain 'T' and resid 120 through 141 removed outlier: 3.575A pdb=" N THR T 124 " --> pdb=" O PRO T 120 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET T 132 " --> pdb=" O ARG T 128 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL T 133 " --> pdb=" O LEU T 129 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP T 141 " --> pdb=" O LEU T 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 163 removed outlier: 3.555A pdb=" N ARG T 162 " --> pdb=" O ALA T 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 173 through 180 removed outlier: 4.051A pdb=" N PHE T 177 " --> pdb=" O LYS T 173 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER T 178 " --> pdb=" O PRO T 174 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP T 179 " --> pdb=" O GLU T 175 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 211 removed outlier: 3.531A pdb=" N ILE T 199 " --> pdb=" O ASP T 195 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU T 201 " --> pdb=" O SER T 197 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU T 202 " --> pdb=" O GLU T 198 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU T 203 " --> pdb=" O ILE T 199 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 229 Processing helix chain 'T' and resid 230 through 240 Processing helix chain 'T' and resid 253 through 269 removed outlier: 3.606A pdb=" N TYR T 269 " --> pdb=" O GLN T 265 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 277 removed outlier: 3.831A pdb=" N GLU T 275 " --> pdb=" O LYS T 271 " (cutoff:3.500A) Processing helix chain 'T' and resid 279 through 302 removed outlier: 3.516A pdb=" N GLN T 295 " --> pdb=" O GLU T 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 303 through 305 No H-bonds generated for 'chain 'T' and resid 303 through 305' Processing helix chain 'T' and resid 312 through 318 Processing helix chain 'T' and resid 344 through 354 Processing helix chain 'T' and resid 361 through 373 removed outlier: 3.687A pdb=" N MET T 366 " --> pdb=" O SER T 362 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR T 367 " --> pdb=" O ASP T 363 " (cutoff:3.500A) Processing helix chain 'T' and resid 375 through 395 removed outlier: 3.501A pdb=" N TYR T 387 " --> pdb=" O LEU T 383 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 425 removed outlier: 3.778A pdb=" N LEU T 417 " --> pdb=" O VAL T 413 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY T 423 " --> pdb=" O ASN T 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET T 425 " --> pdb=" O LEU T 421 " (cutoff:3.500A) Processing helix chain 'T' and resid 425 through 433 removed outlier: 3.882A pdb=" N TYR T 430 " --> pdb=" O LEU T 426 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG T 431 " --> pdb=" O SER T 427 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA T 432 " --> pdb=" O SER T 428 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 458 Processing helix chain 'T' and resid 462 through 466 Processing helix chain 'T' and resid 472 through 490 removed outlier: 3.552A pdb=" N ILE T 480 " --> pdb=" O ARG T 476 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS T 490 " --> pdb=" O VAL T 486 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 503 removed outlier: 3.526A pdb=" N GLN T 499 " --> pdb=" O SER T 495 " (cutoff:3.500A) Processing helix chain 'T' and resid 506 through 515 removed outlier: 3.554A pdb=" N ASN T 512 " --> pdb=" O VAL T 508 " (cutoff:3.500A) Processing helix chain 'T' and resid 526 through 540 removed outlier: 3.790A pdb=" N GLN T 530 " --> pdb=" O GLU T 526 " (cutoff:3.500A) Processing helix chain 'T' and resid 546 through 561 removed outlier: 3.686A pdb=" N TRP T 550 " --> pdb=" O SER T 546 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER T 561 " --> pdb=" O VAL T 557 " (cutoff:3.500A) Processing helix chain 'T' and resid 563 through 567 Processing helix chain 'T' and resid 597 through 608 Processing helix chain 'T' and resid 622 through 636 removed outlier: 3.724A pdb=" N ILE T 626 " --> pdb=" O VAL T 622 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP T 631 " --> pdb=" O GLY T 627 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE T 632 " --> pdb=" O ALA T 628 " (cutoff:3.500A) Processing helix chain 'T' and resid 640 through 646 removed outlier: 4.212A pdb=" N ASN T 644 " --> pdb=" O SER T 640 " (cutoff:3.500A) Processing helix chain 'T' and resid 703 through 726 removed outlier: 3.606A pdb=" N TRP T 716 " --> pdb=" O LYS T 712 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN T 721 " --> pdb=" O LEU T 717 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLU T 722 " --> pdb=" O LYS T 718 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE T 723 " --> pdb=" O ASN T 719 " (cutoff:3.500A) Processing helix chain 'T' and resid 730 through 752 removed outlier: 3.597A pdb=" N TRP T 738 " --> pdb=" O ILE T 734 " (cutoff:3.500A) Processing helix chain 'T' and resid 770 through 790 removed outlier: 3.682A pdb=" N ILE T 774 " --> pdb=" O ASN T 770 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET T 775 " --> pdb=" O ALA T 771 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE T 782 " --> pdb=" O ASN T 778 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU T 783 " --> pdb=" O VAL T 779 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL T 786 " --> pdb=" O PHE T 782 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU T 787 " --> pdb=" O LEU T 783 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL T 788 " --> pdb=" O HIS T 784 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU T 789 " --> pdb=" O ALA T 785 " (cutoff:3.500A) Processing helix chain 'T' and resid 814 through 830 Processing helix chain 'T' and resid 839 through 844 Processing helix chain 'T' and resid 851 through 856 removed outlier: 3.916A pdb=" N ILE T 855 " --> pdb=" O LEU T 851 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE T 856 " --> pdb=" O HIS T 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 851 through 856' Processing helix chain 'T' and resid 866 through 883 removed outlier: 4.156A pdb=" N LYS T 870 " --> pdb=" O LYS T 866 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER T 873 " --> pdb=" O ASN T 869 " (cutoff:3.500A) Processing helix chain 'T' and resid 888 through 898 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 5.804A pdb=" N ILE A 14 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LYS A 331 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE A 16 " --> pdb=" O LYS A 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.300A pdb=" N LYS A 105 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR A 219 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 609 through 611 removed outlier: 3.891A pdb=" N VAL A 611 " --> pdb=" O MET A 617 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 81 through 84 Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 149 removed outlier: 7.582A pdb=" N LEU B 148 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 353 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG B 351 " --> pdb=" O GLU B 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 154 removed outlier: 6.108A pdb=" N GLN B 153 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY B 355 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N HIS B 421 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE B 357 " --> pdb=" O HIS B 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.832A pdb=" N TYR B 252 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 6.868A pdb=" N TYR B 497 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 528 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 703 " --> pdb=" O CYS B 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 548 through 552 Processing sheet with id=AB1, first strand: chain 'C' and resid 81 through 84 Processing sheet with id=AB2, first strand: chain 'C' and resid 148 through 154 removed outlier: 7.579A pdb=" N LEU C 148 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 353 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU C 150 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY C 355 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N HIS C 152 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG C 351 " --> pdb=" O GLU C 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.668A pdb=" N ILE C 245 " --> pdb=" O TYR C 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 421 through 422 Processing sheet with id=AB5, first strand: chain 'C' and resid 527 through 529 removed outlier: 6.159A pdb=" N ILE C 703 " --> pdb=" O CYS C 744 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 548 through 552 removed outlier: 3.571A pdb=" N MET C 551 " --> pdb=" O VAL C 673 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AB8, first strand: chain 'D' and resid 148 through 154 removed outlier: 7.510A pdb=" N LEU D 148 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 353 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 150 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY D 355 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N HIS D 152 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N PHE D 357 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N HIS D 154 " --> pdb=" O PHE D 357 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG D 351 " --> pdb=" O GLU D 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 148 through 154 removed outlier: 7.510A pdb=" N LEU D 148 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU D 353 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 150 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY D 355 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N HIS D 152 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N PHE D 357 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N HIS D 154 " --> pdb=" O PHE D 357 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL D 419 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLY D 355 " --> pdb=" O VAL D 419 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N HIS D 421 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N PHE D 357 " --> pdb=" O HIS D 421 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL D 466 " --> pdb=" O THR D 496 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N HIS D 498 " --> pdb=" O VAL D 466 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA D 468 " --> pdb=" O HIS D 498 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE D 495 " --> pdb=" O ARG D 527 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLY D 529 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TYR D 497 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU D 528 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE D 703 " --> pdb=" O CYS D 744 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AC2, first strand: chain 'D' and resid 548 through 552 Processing sheet with id=AC3, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC4, first strand: chain 'E' and resid 148 through 154 removed outlier: 7.527A pdb=" N LEU E 148 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU E 353 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLU E 150 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLY E 355 " --> pdb=" O GLU E 150 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N HIS E 152 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N PHE E 357 " --> pdb=" O HIS E 152 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N HIS E 154 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG E 351 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ALA E 417 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU E 353 " --> pdb=" O ALA E 417 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 419 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY E 355 " --> pdb=" O VAL E 419 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N HIS E 421 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE E 357 " --> pdb=" O HIS E 421 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 245 through 247 removed outlier: 3.811A pdb=" N ILE E 245 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR E 252 " --> pdb=" O ILE E 245 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS E 247 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 496 through 498 removed outlier: 3.544A pdb=" N TYR E 497 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE E 703 " --> pdb=" O CYS E 744 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 548 through 552 Processing sheet with id=AC8, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC9, first strand: chain 'F' and resid 148 through 153 removed outlier: 5.862A pdb=" N LEU F 148 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR F 352 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU F 354 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N HIS F 152 " --> pdb=" O GLU F 354 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 244 through 247 Processing sheet with id=AD2, first strand: chain 'F' and resid 421 through 422 Processing sheet with id=AD3, first strand: chain 'F' and resid 496 through 498 removed outlier: 6.724A pdb=" N TYR F 497 " --> pdb=" O GLY F 529 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 528 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE F 703 " --> pdb=" O CYS F 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 548 through 552 Processing sheet with id=AD5, first strand: chain 'G' and resid 81 through 84 Processing sheet with id=AD6, first strand: chain 'G' and resid 148 through 154 removed outlier: 4.550A pdb=" N HIS G 149 " --> pdb=" O TYR G 352 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU G 354 " --> pdb=" O HIS G 149 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR G 151 " --> pdb=" O GLU G 354 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG G 356 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLN G 153 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG G 351 " --> pdb=" O GLU G 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 148 through 154 removed outlier: 4.550A pdb=" N HIS G 149 " --> pdb=" O TYR G 352 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLU G 354 " --> pdb=" O HIS G 149 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR G 151 " --> pdb=" O GLU G 354 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG G 356 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLN G 153 " --> pdb=" O ARG G 356 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL G 419 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY G 355 " --> pdb=" O VAL G 419 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N HIS G 421 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE G 357 " --> pdb=" O HIS G 421 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 245 through 247 removed outlier: 4.083A pdb=" N ILE G 245 " --> pdb=" O TYR G 252 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 496 through 498 removed outlier: 7.055A pdb=" N TYR G 497 " --> pdb=" O GLY G 529 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU G 528 " --> pdb=" O GLU G 704 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE G 703 " --> pdb=" O CYS G 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'G' and resid 548 through 552 Processing sheet with id=AE2, first strand: chain 'I' and resid 81 through 84 removed outlier: 3.576A pdb=" N LYS I 89 " --> pdb=" O LYS I 82 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 148 through 154 removed outlier: 7.486A pdb=" N LEU I 148 " --> pdb=" O ARG I 351 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU I 353 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU I 150 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY I 355 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS I 152 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N PHE I 357 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N HIS I 154 " --> pdb=" O PHE I 357 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 148 through 154 removed outlier: 7.486A pdb=" N LEU I 148 " --> pdb=" O ARG I 351 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU I 353 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU I 150 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY I 355 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N HIS I 152 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N PHE I 357 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N HIS I 154 " --> pdb=" O PHE I 357 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL I 419 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY I 355 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS I 421 " --> pdb=" O GLY I 355 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N PHE I 357 " --> pdb=" O HIS I 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'I' and resid 244 through 246 removed outlier: 3.608A pdb=" N ILE I 245 " --> pdb=" O TYR I 252 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR I 252 " --> pdb=" O ILE I 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 527 through 529 Processing sheet with id=AE7, first strand: chain 'I' and resid 548 through 552 Processing sheet with id=AE8, first strand: chain 'J' and resid 81 through 84 Processing sheet with id=AE9, first strand: chain 'J' and resid 148 through 154 removed outlier: 7.703A pdb=" N LEU J 148 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU J 353 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU J 150 " --> pdb=" O LEU J 353 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY J 355 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS J 152 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 9.828A pdb=" N PHE J 357 " --> pdb=" O HIS J 152 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N HIS J 154 " --> pdb=" O PHE J 357 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG J 351 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALA J 417 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU J 353 " --> pdb=" O ALA J 417 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL J 419 " --> pdb=" O LEU J 353 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLY J 355 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS J 421 " --> pdb=" O GLY J 355 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE J 357 " --> pdb=" O HIS J 421 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL J 466 " --> pdb=" O THR J 496 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N HIS J 498 " --> pdb=" O VAL J 466 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA J 468 " --> pdb=" O HIS J 498 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG J 527 " --> pdb=" O PHE J 495 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 245 through 246 Processing sheet with id=AF2, first strand: chain 'J' and resid 548 through 552 Processing sheet with id=AF3, first strand: chain 'J' and resid 703 through 704 removed outlier: 5.970A pdb=" N ILE J 703 " --> pdb=" O CYS J 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'K' and resid 81 through 84 Processing sheet with id=AF5, first strand: chain 'K' and resid 148 through 154 removed outlier: 4.937A pdb=" N HIS K 149 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU K 354 " --> pdb=" O HIS K 149 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR K 151 " --> pdb=" O GLU K 354 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ARG K 356 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN K 153 " --> pdb=" O ARG K 356 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 148 through 154 removed outlier: 4.937A pdb=" N HIS K 149 " --> pdb=" O TYR K 352 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU K 354 " --> pdb=" O HIS K 149 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR K 151 " --> pdb=" O GLU K 354 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ARG K 356 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN K 153 " --> pdb=" O ARG K 356 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL K 419 " --> pdb=" O LEU K 353 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY K 355 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N HIS K 421 " --> pdb=" O GLY K 355 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE K 357 " --> pdb=" O HIS K 421 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL K 466 " --> pdb=" O THR K 496 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N HIS K 498 " --> pdb=" O VAL K 466 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA K 468 " --> pdb=" O HIS K 498 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE K 495 " --> pdb=" O ARG K 527 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY K 529 " --> pdb=" O PHE K 495 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR K 497 " --> pdb=" O GLY K 529 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE K 703 " --> pdb=" O CYS K 744 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 548 through 552 Processing sheet with id=AF8, first strand: chain 'L' and resid 81 through 84 Processing sheet with id=AF9, first strand: chain 'L' and resid 148 through 154 removed outlier: 7.697A pdb=" N LEU L 148 " --> pdb=" O ARG L 351 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU L 353 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU L 150 " --> pdb=" O LEU L 353 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY L 355 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N HIS L 152 " --> pdb=" O GLY L 355 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N PHE L 357 " --> pdb=" O HIS L 152 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N HIS L 154 " --> pdb=" O PHE L 357 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG L 351 " --> pdb=" O GLU L 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 148 through 154 removed outlier: 7.697A pdb=" N LEU L 148 " --> pdb=" O ARG L 351 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU L 353 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU L 150 " --> pdb=" O LEU L 353 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY L 355 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N HIS L 152 " --> pdb=" O GLY L 355 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N PHE L 357 " --> pdb=" O HIS L 152 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N HIS L 154 " --> pdb=" O PHE L 357 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL L 419 " --> pdb=" O LEU L 353 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY L 355 " --> pdb=" O VAL L 419 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS L 421 " --> pdb=" O GLY L 355 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N PHE L 357 " --> pdb=" O HIS L 421 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 245 through 246 Processing sheet with id=AG3, first strand: chain 'L' and resid 527 through 529 Processing sheet with id=AG4, first strand: chain 'L' and resid 548 through 552 Processing sheet with id=AG5, first strand: chain 'M' and resid 81 through 84 Processing sheet with id=AG6, first strand: chain 'M' and resid 148 through 149 removed outlier: 7.637A pdb=" N LEU M 148 " --> pdb=" O ARG M 351 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU M 353 " --> pdb=" O LEU M 148 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG M 351 " --> pdb=" O GLU M 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'M' and resid 153 through 154 removed outlier: 6.107A pdb=" N GLN M 153 " --> pdb=" O ARG M 356 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY M 355 " --> pdb=" O VAL M 419 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N HIS M 421 " --> pdb=" O GLY M 355 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE M 357 " --> pdb=" O HIS M 421 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 496 through 498 removed outlier: 6.693A pdb=" N TYR M 497 " --> pdb=" O GLY M 529 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU M 528 " --> pdb=" O GLU M 704 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE M 703 " --> pdb=" O CYS M 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'M' and resid 548 through 552 Processing sheet with id=AH1, first strand: chain 'N' and resid 81 through 84 Processing sheet with id=AH2, first strand: chain 'N' and resid 148 through 149 removed outlier: 7.643A pdb=" N LEU N 148 " --> pdb=" O ARG N 351 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU N 353 " --> pdb=" O LEU N 148 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 153 through 154 removed outlier: 5.800A pdb=" N GLN N 153 " --> pdb=" O ARG N 356 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY N 355 " --> pdb=" O VAL N 419 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS N 421 " --> pdb=" O GLY N 355 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE N 357 " --> pdb=" O HIS N 421 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 245 through 246 Processing sheet with id=AH5, first strand: chain 'N' and resid 496 through 498 removed outlier: 3.504A pdb=" N TYR N 497 " --> pdb=" O ARG N 527 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU N 528 " --> pdb=" O GLU N 704 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE N 703 " --> pdb=" O CYS N 744 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 548 through 552 Processing sheet with id=AH7, first strand: chain 'O' and resid 14 through 17 removed outlier: 6.872A pdb=" N ILE O 14 " --> pdb=" O LYS O 329 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LYS O 331 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE O 16 " --> pdb=" O LYS O 331 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE O 342 " --> pdb=" O VAL O 330 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 104 through 106 removed outlier: 6.609A pdb=" N LYS O 105 " --> pdb=" O LEU O 217 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR O 219 " --> pdb=" O LYS O 105 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE O 216 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL O 249 " --> pdb=" O ILE O 216 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE O 218 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N THR O 251 " --> pdb=" O ILE O 218 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY O 252 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 609 through 611 removed outlier: 3.561A pdb=" N SER O 609 " --> pdb=" O PHE O 619 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL O 611 " --> pdb=" O MET O 617 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET O 617 " --> pdb=" O VAL O 611 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 104 through 106 removed outlier: 5.682A pdb=" N ILE P 216 " --> pdb=" O VAL P 247 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL P 249 " --> pdb=" O ILE P 216 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE P 218 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR P 251 " --> pdb=" O ILE P 218 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY P 252 " --> pdb=" O VAL P 74 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE P 308 " --> pdb=" O VAL P 71 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE P 73 " --> pdb=" O ILE P 308 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 609 through 612 removed outlier: 3.754A pdb=" N MET P 617 " --> pdb=" O VAL P 611 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 15 through 17 removed outlier: 6.978A pdb=" N ILE Q 16 " --> pdb=" O LYS Q 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'Q' and resid 104 through 106 removed outlier: 5.820A pdb=" N ILE Q 216 " --> pdb=" O VAL Q 247 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL Q 249 " --> pdb=" O ILE Q 216 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE Q 218 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR Q 251 " --> pdb=" O ILE Q 218 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE Q 72 " --> pdb=" O ALA Q 250 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLY Q 252 " --> pdb=" O PHE Q 72 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL Q 74 " --> pdb=" O GLY Q 252 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ILE Q 308 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE Q 73 " --> pdb=" O ILE Q 308 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 575 through 576 removed outlier: 4.240A pdb=" N ASP Q 618 " --> pdb=" O LEU Q 576 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET Q 617 " --> pdb=" O VAL Q 611 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL Q 611 " --> pdb=" O MET Q 617 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 14 through 17 removed outlier: 6.186A pdb=" N ILE R 14 " --> pdb=" O LYS R 329 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS R 331 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE R 16 " --> pdb=" O LYS R 331 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 330 " --> pdb=" O ILE R 342 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE R 342 " --> pdb=" O VAL R 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'R' and resid 104 through 106 removed outlier: 7.013A pdb=" N LYS R 105 " --> pdb=" O LEU R 217 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N THR R 219 " --> pdb=" O LYS R 105 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'R' and resid 569 through 570 Processing sheet with id=AI9, first strand: chain 'R' and resid 610 through 612 Processing sheet with id=AJ1, first strand: chain 'S' and resid 14 through 17 removed outlier: 6.495A pdb=" N ILE S 14 " --> pdb=" O LYS S 329 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LYS S 331 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE S 16 " --> pdb=" O LYS S 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'S' and resid 105 through 106 removed outlier: 7.388A pdb=" N LYS S 105 " --> pdb=" O LEU S 217 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR S 219 " --> pdb=" O LYS S 105 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE S 72 " --> pdb=" O ALA S 250 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE S 308 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N PHE S 73 " --> pdb=" O ILE S 308 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'S' and resid 569 through 570 Processing sheet with id=AJ4, first strand: chain 'S' and resid 608 through 612 removed outlier: 3.633A pdb=" N MET S 617 " --> pdb=" O VAL S 611 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'T' and resid 14 through 17 removed outlier: 5.681A pdb=" N ILE T 14 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS T 331 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE T 16 " --> pdb=" O LYS T 331 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'T' and resid 104 through 106 removed outlier: 6.405A pdb=" N LYS T 105 " --> pdb=" O LEU T 217 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR T 219 " --> pdb=" O LYS T 105 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ILE T 216 " --> pdb=" O VAL T 247 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL T 249 " --> pdb=" O ILE T 216 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE T 218 " --> pdb=" O VAL T 249 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N THR T 251 " --> pdb=" O ILE T 218 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE T 72 " --> pdb=" O ALA T 250 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLY T 252 " --> pdb=" O PHE T 72 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL T 74 " --> pdb=" O GLY T 252 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'T' and resid 609 through 610 6065 hydrogen bonds defined for protein. 17532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 53.98 Time building geometry restraints manager: 42.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 39382 1.34 - 1.46: 17985 1.46 - 1.58: 66041 1.58 - 1.70: 0 1.70 - 1.82: 929 Bond restraints: 124337 Sorted by residual: bond pdb=" N ILE P 656 " pdb=" CA ILE P 656 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.11e-02 8.12e+03 1.14e+01 bond pdb=" N VAL S 569 " pdb=" CA VAL S 569 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.15e-02 7.56e+03 8.93e+00 bond pdb=" N ASN A 597 " pdb=" CA ASN A 597 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.16e-02 7.43e+03 8.87e+00 bond pdb=" N VAL T 611 " pdb=" CA VAL T 611 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.33e+00 bond pdb=" N MET T 617 " pdb=" CA MET T 617 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.21e-02 6.83e+03 8.11e+00 ... (remaining 124332 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.45: 2382 105.45 - 112.61: 64691 112.61 - 119.77: 41465 119.77 - 126.94: 57944 126.94 - 134.10: 1767 Bond angle restraints: 168249 Sorted by residual: angle pdb=" N VAL K 23 " pdb=" CA VAL K 23 " pdb=" C VAL K 23 " ideal model delta sigma weight residual 113.10 108.39 4.71 9.70e-01 1.06e+00 2.36e+01 angle pdb=" N GLY L 430 " pdb=" CA GLY L 430 " pdb=" C GLY L 430 " ideal model delta sigma weight residual 110.96 116.46 -5.50 1.19e+00 7.06e-01 2.14e+01 angle pdb=" N VAL P 133 " pdb=" CA VAL P 133 " pdb=" C VAL P 133 " ideal model delta sigma weight residual 113.42 108.15 5.27 1.17e+00 7.31e-01 2.03e+01 angle pdb=" N VAL P 811 " pdb=" CA VAL P 811 " pdb=" C VAL P 811 " ideal model delta sigma weight residual 111.90 108.54 3.36 8.10e-01 1.52e+00 1.72e+01 angle pdb=" N ILE R 544 " pdb=" CA ILE R 544 " pdb=" C ILE R 544 " ideal model delta sigma weight residual 106.21 110.58 -4.37 1.07e+00 8.73e-01 1.67e+01 ... (remaining 168244 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 67487 18.01 - 36.02: 6536 36.02 - 54.03: 978 54.03 - 72.05: 189 72.05 - 90.06: 106 Dihedral angle restraints: 75296 sinusoidal: 30845 harmonic: 44451 Sorted by residual: dihedral pdb=" CA ASN A 647 " pdb=" C ASN A 647 " pdb=" N LYS A 648 " pdb=" CA LYS A 648 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA THR J 647 " pdb=" C THR J 647 " pdb=" N GLY J 648 " pdb=" CA GLY J 648 " ideal model delta harmonic sigma weight residual -180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA TYR D 433 " pdb=" C TYR D 433 " pdb=" N PRO D 434 " pdb=" CA PRO D 434 " ideal model delta harmonic sigma weight residual 180.00 -160.61 -19.39 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 75293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 14266 0.042 - 0.084: 3363 0.084 - 0.125: 885 0.125 - 0.167: 42 0.167 - 0.209: 12 Chirality restraints: 18568 Sorted by residual: chirality pdb=" CA GLU Q 279 " pdb=" N GLU Q 279 " pdb=" C GLU Q 279 " pdb=" CB GLU Q 279 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE P 656 " pdb=" N ILE P 656 " pdb=" C ILE P 656 " pdb=" CB ILE P 656 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LEU A 599 " pdb=" N LEU A 599 " pdb=" C LEU A 599 " pdb=" CB LEU A 599 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 18565 not shown) Planarity restraints: 21596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 408 " -0.091 5.00e-02 4.00e+02 1.37e-01 3.00e+01 pdb=" N PRO B 409 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 738 " -0.025 2.00e-02 2.50e+03 1.84e-02 8.51e+00 pdb=" CG TRP Q 738 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 738 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 738 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 738 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 738 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 738 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 738 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 738 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 738 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 230 " -0.018 2.00e-02 2.50e+03 1.54e-02 5.93e+00 pdb=" CG TRP F 230 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP F 230 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 230 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 230 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 230 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 230 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 230 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 230 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 230 " -0.000 2.00e-02 2.50e+03 ... (remaining 21593 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1937 2.66 - 3.22: 121144 3.22 - 3.78: 194684 3.78 - 4.34: 265616 4.34 - 4.90: 419975 Nonbonded interactions: 1003356 Sorted by model distance: nonbonded pdb=" O ILE L 195 " pdb=" OD1 ASP L 196 " model vdw 2.099 3.040 nonbonded pdb=" OE1 GLN A 159 " pdb=" OH TYR A 189 " model vdw 2.196 2.440 nonbonded pdb=" O GLY Q 735 " pdb=" OG SER Q 739 " model vdw 2.205 2.440 nonbonded pdb=" OG SER N 548 " pdb=" OE2 GLU N 674 " model vdw 2.205 2.440 nonbonded pdb=" OE2 GLU N 269 " pdb=" OH TYR N 295 " model vdw 2.207 2.440 ... (remaining 1003351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = (chain 'B' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'C' and (resid 1 through 310 or resid 329 through 640 or (resid 641 and ( \ name N or name CA or name C or name O or name CB )) or resid 642 through 798)) selection = (chain 'D' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'E' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'F' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'G' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'I' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'J' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'K' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'L' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) selection = (chain 'M' and (resid 1 through 310 or (resid 329 through 330 and (name N or nam \ e CA or name C or name O or name CB )) or resid 331 through 615 or (resid 616 th \ rough 617 and (name N or name CA or name C or name O or name CB )) or resid 631 \ through 798)) selection = (chain 'N' and (resid 1 through 310 or resid 329 through 617 or resid 631 throug \ h 798)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 19.590 Check model and map are aligned: 1.330 Set scattering table: 0.860 Process input model: 249.760 Find NCS groups from input model: 8.170 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 286.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 124337 Z= 0.143 Angle : 0.524 10.120 168249 Z= 0.281 Chirality : 0.038 0.209 18568 Planarity : 0.003 0.137 21596 Dihedral : 14.322 90.058 46430 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.07 % Allowed : 0.32 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.07), residues: 14986 helix: 0.51 (0.06), residues: 8206 sheet: -1.09 (0.20), residues: 701 loop : -0.89 (0.08), residues: 6079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP Q 738 HIS 0.009 0.001 HIS K 796 PHE 0.021 0.001 PHE A 743 TYR 0.024 0.001 TYR K 433 ARG 0.015 0.000 ARG O 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1001 time to evaluate : 11.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 VAL cc_start: 0.6827 (OUTLIER) cc_final: 0.6591 (m) REVERT: B 428 LYS cc_start: 0.6997 (mmtt) cc_final: 0.6784 (mmtt) REVERT: B 551 MET cc_start: 0.8167 (ptt) cc_final: 0.7878 (ptt) REVERT: B 744 CYS cc_start: 0.8294 (m) cc_final: 0.8049 (m) REVERT: C 92 LEU cc_start: 0.8803 (tp) cc_final: 0.8558 (tp) REVERT: C 204 PHE cc_start: 0.7770 (t80) cc_final: 0.7361 (t80) REVERT: C 696 MET cc_start: 0.8254 (tpp) cc_final: 0.7976 (mmm) REVERT: D 102 MET cc_start: 0.9121 (mmp) cc_final: 0.8897 (mmp) REVERT: D 574 LEU cc_start: 0.8324 (mt) cc_final: 0.7949 (mt) REVERT: E 450 MET cc_start: 0.8841 (mmp) cc_final: 0.8357 (mmm) REVERT: F 609 MET cc_start: 0.7796 (ppp) cc_final: 0.7031 (ppp) REVERT: G 102 MET cc_start: 0.8520 (mmm) cc_final: 0.8162 (mmp) REVERT: J 741 MET cc_start: 0.7555 (mtt) cc_final: 0.7092 (mtt) REVERT: L 387 MET cc_start: 0.7149 (ppp) cc_final: 0.6941 (ppp) REVERT: M 92 LEU cc_start: 0.9336 (mt) cc_final: 0.9117 (mm) REVERT: N 741 MET cc_start: 0.7634 (mtt) cc_final: 0.7421 (mtp) REVERT: O 170 LYS cc_start: 0.8054 (tttt) cc_final: 0.7590 (mmtm) REVERT: O 309 GLN cc_start: 0.6392 (pp30) cc_final: 0.6071 (pp30) REVERT: P 758 ARG cc_start: 0.3841 (ttt180) cc_final: 0.3528 (ttm170) REVERT: Q 78 ARG cc_start: 0.3759 (tmm160) cc_final: 0.2898 (tmm160) REVERT: Q 500 MET cc_start: 0.7242 (ppp) cc_final: 0.6928 (ppp) REVERT: R 431 ARG cc_start: 0.3996 (ttp-170) cc_final: 0.3241 (ttp-170) REVERT: R 573 MET cc_start: 0.3823 (ttp) cc_final: 0.3386 (ttp) REVERT: R 775 MET cc_start: 0.6161 (ptt) cc_final: 0.4806 (ttt) REVERT: S 539 MET cc_start: 0.1007 (ptt) cc_final: -0.0960 (tpp) REVERT: T 202 GLU cc_start: 0.8187 (pm20) cc_final: 0.7943 (pm20) REVERT: T 616 LEU cc_start: 0.2188 (OUTLIER) cc_final: 0.1954 (mm) outliers start: 9 outliers final: 0 residues processed: 1009 average time/residue: 0.9749 time to fit residues: 1729.9908 Evaluate side-chains 694 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 692 time to evaluate : 10.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain T residue 616 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1271 optimal weight: 8.9990 chunk 1141 optimal weight: 9.9990 chunk 633 optimal weight: 1.9990 chunk 389 optimal weight: 4.9990 chunk 769 optimal weight: 5.9990 chunk 609 optimal weight: 9.9990 chunk 1180 optimal weight: 0.9990 chunk 456 optimal weight: 1.9990 chunk 717 optimal weight: 7.9990 chunk 878 optimal weight: 0.8980 chunk 1367 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 384 HIS D 445 GLN D 570 HIS ** D 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 HIS ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 787 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS J 787 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 GLN K 789 ASN ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 171 HIS ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 ASN ** O 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 381 GLN ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 624 ASN ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 226 GLN ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 374 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 477 ASN T 614 ASN ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 124337 Z= 0.197 Angle : 0.562 10.843 168249 Z= 0.293 Chirality : 0.040 0.205 18568 Planarity : 0.004 0.087 21596 Dihedral : 4.101 20.287 16472 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.49 % Allowed : 6.68 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.07), residues: 14986 helix: 0.87 (0.06), residues: 8491 sheet: -1.11 (0.21), residues: 646 loop : -0.86 (0.08), residues: 5849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Q 738 HIS 0.011 0.001 HIS L 474 PHE 0.028 0.001 PHE A 743 TYR 0.032 0.001 TYR L 433 ARG 0.007 0.000 ARG O 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 801 time to evaluate : 10.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 SER cc_start: 0.7981 (m) cc_final: 0.7287 (t) REVERT: B 428 LYS cc_start: 0.7091 (mmtt) cc_final: 0.6849 (mmtt) REVERT: B 551 MET cc_start: 0.8259 (ptt) cc_final: 0.7955 (ptm) REVERT: B 744 CYS cc_start: 0.8535 (m) cc_final: 0.8245 (m) REVERT: D 335 LEU cc_start: 0.8672 (tp) cc_final: 0.8410 (tt) REVERT: E 450 MET cc_start: 0.8639 (mmp) cc_final: 0.8167 (mmm) REVERT: E 695 LYS cc_start: 0.7232 (ttmm) cc_final: 0.7001 (ttmm) REVERT: E 760 GLU cc_start: 0.7298 (tp30) cc_final: 0.6940 (tp30) REVERT: F 65 MET cc_start: 0.8166 (ppp) cc_final: 0.7919 (ppp) REVERT: F 649 MET cc_start: 0.7474 (mmp) cc_final: 0.7242 (mmp) REVERT: G 642 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: I 741 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (ttm) REVERT: J 526 ASP cc_start: 0.6894 (m-30) cc_final: 0.6411 (m-30) REVERT: J 741 MET cc_start: 0.7358 (mtt) cc_final: 0.6778 (mtt) REVERT: K 741 MET cc_start: 0.8198 (mtp) cc_final: 0.7570 (mtp) REVERT: M 150 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7977 (tm-30) REVERT: N 366 MET cc_start: 0.7978 (tmm) cc_final: 0.7636 (tmm) REVERT: O 170 LYS cc_start: 0.8150 (tttt) cc_final: 0.7672 (mmtm) REVERT: O 256 LEU cc_start: 0.8748 (mt) cc_final: 0.8413 (mt) REVERT: O 775 MET cc_start: 0.4371 (tpp) cc_final: 0.3922 (ptm) REVERT: P 165 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5306 (t70) REVERT: P 617 MET cc_start: 0.1155 (tpp) cc_final: -0.0907 (ttm) REVERT: P 758 ARG cc_start: 0.3843 (ttt180) cc_final: 0.3528 (ttm170) REVERT: Q 78 ARG cc_start: 0.3814 (tmm160) cc_final: 0.3002 (tmm160) REVERT: Q 732 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5851 (mt) REVERT: R 443 MET cc_start: 0.3704 (tmm) cc_final: 0.3409 (tmm) REVERT: R 775 MET cc_start: 0.6301 (ptt) cc_final: 0.4893 (ttt) REVERT: S 132 MET cc_start: 0.6806 (mtt) cc_final: 0.6465 (mtt) REVERT: S 500 MET cc_start: 0.3752 (mmt) cc_final: 0.3538 (mmt) REVERT: S 539 MET cc_start: 0.1177 (ptt) cc_final: -0.0894 (tpp) outliers start: 65 outliers final: 37 residues processed: 843 average time/residue: 1.0079 time to fit residues: 1506.0732 Evaluate side-chains 710 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 669 time to evaluate : 10.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 786 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 642 GLU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain J residue 481 CYS Chi-restraints excluded: chain J residue 551 MET Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 549 LEU Chi-restraints excluded: chain M residue 655 LEU Chi-restraints excluded: chain N residue 64 ASN Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 549 LEU Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain P residue 165 HIS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 656 ILE Chi-restraints excluded: chain Q residue 170 LYS Chi-restraints excluded: chain Q residue 732 LEU Chi-restraints excluded: chain S residue 608 LEU Chi-restraints excluded: chain S residue 721 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 760 optimal weight: 9.9990 chunk 424 optimal weight: 9.9990 chunk 1138 optimal weight: 6.9990 chunk 931 optimal weight: 10.0000 chunk 377 optimal weight: 1.9990 chunk 1370 optimal weight: 10.0000 chunk 1480 optimal weight: 5.9990 chunk 1220 optimal weight: 30.0000 chunk 1358 optimal weight: 10.0000 chunk 467 optimal weight: 8.9990 chunk 1099 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN B 789 ASN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN ** D 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 266 GLN ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS K 7 ASN ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 445 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 GLN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 552 ASN ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 226 GLN ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN P 461 ASN ** P 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 369 ASN R 624 ASN ** R 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 315 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 907 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 124337 Z= 0.300 Angle : 0.593 10.687 168249 Z= 0.305 Chirality : 0.041 0.191 18568 Planarity : 0.004 0.071 21596 Dihedral : 4.295 21.001 16469 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.02 % Allowed : 10.51 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.07), residues: 14986 helix: 0.82 (0.06), residues: 8549 sheet: -1.26 (0.21), residues: 644 loop : -0.97 (0.08), residues: 5793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 659 HIS 0.013 0.001 HIS A 784 PHE 0.032 0.002 PHE P 451 TYR 0.030 0.002 TYR L 433 ARG 0.009 0.000 ARG O 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 730 time to evaluate : 10.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 SER cc_start: 0.7906 (m) cc_final: 0.7286 (t) REVERT: B 428 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6913 (mmtt) REVERT: B 551 MET cc_start: 0.8477 (ptt) cc_final: 0.8244 (ptm) REVERT: E 366 MET cc_start: 0.8560 (ppp) cc_final: 0.8339 (ppp) REVERT: E 450 MET cc_start: 0.8697 (mmp) cc_final: 0.8305 (mmm) REVERT: F 65 MET cc_start: 0.8120 (ppp) cc_final: 0.7905 (ppp) REVERT: F 609 MET cc_start: 0.8051 (ppp) cc_final: 0.7540 (ppp) REVERT: G 135 TYR cc_start: 0.7671 (t80) cc_final: 0.7446 (t80) REVERT: I 65 MET cc_start: 0.8332 (ptt) cc_final: 0.8049 (ptp) REVERT: J 526 ASP cc_start: 0.6801 (m-30) cc_final: 0.6441 (m-30) REVERT: J 741 MET cc_start: 0.7688 (mtt) cc_final: 0.7239 (mtt) REVERT: K 65 MET cc_start: 0.8003 (ppp) cc_final: 0.7162 (ptt) REVERT: L 102 MET cc_start: 0.8705 (mmm) cc_final: 0.8315 (tpp) REVERT: M 150 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7945 (tm-30) REVERT: O 170 LYS cc_start: 0.8233 (tttt) cc_final: 0.7723 (mmtm) REVERT: O 256 LEU cc_start: 0.8765 (mt) cc_final: 0.8565 (mt) REVERT: P 617 MET cc_start: 0.1132 (tpp) cc_final: -0.0773 (ttm) REVERT: P 758 ARG cc_start: 0.3806 (ttt180) cc_final: 0.3512 (ttm170) REVERT: Q 78 ARG cc_start: 0.4052 (tmm160) cc_final: 0.3227 (tmm160) REVERT: R 443 MET cc_start: 0.4096 (tmm) cc_final: 0.3775 (tmm) REVERT: R 539 MET cc_start: 0.0552 (OUTLIER) cc_final: -0.0044 (tmm) REVERT: R 775 MET cc_start: 0.6359 (ptt) cc_final: 0.4991 (ttt) REVERT: S 30 ASP cc_start: 0.5883 (t70) cc_final: 0.5539 (t70) REVERT: S 132 MET cc_start: 0.7278 (mtt) cc_final: 0.6952 (mtt) REVERT: S 425 MET cc_start: 0.5922 (tpt) cc_final: 0.5575 (tpt) REVERT: S 539 MET cc_start: 0.1477 (ptt) cc_final: -0.0921 (tpp) REVERT: T 289 MET cc_start: 0.7462 (mmm) cc_final: 0.7224 (mmm) REVERT: T 366 MET cc_start: 0.7379 (ppp) cc_final: 0.5944 (tpp) REVERT: T 510 ILE cc_start: 0.8988 (mm) cc_final: 0.8701 (mt) outliers start: 135 outliers final: 78 residues processed: 827 average time/residue: 0.9787 time to fit residues: 1439.6407 Evaluate side-chains 742 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 663 time to evaluate : 9.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 682 ASP Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 531 CYS Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 385 MET Chi-restraints excluded: chain E residue 786 VAL Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 340 HIS Chi-restraints excluded: chain I residue 757 LEU Chi-restraints excluded: chain J residue 481 CYS Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 293 TRP Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 373 VAL Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 549 LEU Chi-restraints excluded: chain M residue 655 LEU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 701 ILE Chi-restraints excluded: chain N residue 64 ASN Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 739 VAL Chi-restraints excluded: chain N residue 781 ARG Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 450 ILE Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain O residue 812 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 454 VAL Chi-restraints excluded: chain P residue 656 ILE Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 732 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain S residue 234 LEU Chi-restraints excluded: chain S residue 280 SER Chi-restraints excluded: chain S residue 721 ASN Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 854 PHE Chi-restraints excluded: chain T residue 907 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1353 optimal weight: 0.7980 chunk 1030 optimal weight: 20.0000 chunk 711 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 653 optimal weight: 0.6980 chunk 919 optimal weight: 5.9990 chunk 1374 optimal weight: 0.3980 chunk 1455 optimal weight: 30.0000 chunk 718 optimal weight: 1.9990 chunk 1303 optimal weight: 5.9990 chunk 392 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 715 GLN A 719 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN C 213 ASN C 787 ASN D 787 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 HIS ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 444 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 789 ASN ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 605 GLN N 668 GLN O 155 ASN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 513 GLN ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN P 485 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 778 ASN T 194 GLN T 315 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 124337 Z= 0.155 Angle : 0.513 12.630 168249 Z= 0.262 Chirality : 0.039 0.282 18568 Planarity : 0.004 0.060 21596 Dihedral : 4.081 20.400 16469 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.10 % Allowed : 12.30 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.07), residues: 14986 helix: 1.08 (0.06), residues: 8505 sheet: -1.08 (0.21), residues: 627 loop : -0.91 (0.08), residues: 5854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 659 HIS 0.011 0.001 HIS A 784 PHE 0.033 0.001 PHE P 451 TYR 0.027 0.001 TYR L 433 ARG 0.009 0.000 ARG O 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 769 time to evaluate : 9.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7941 (mp0) cc_final: 0.7552 (mp0) REVERT: A 280 SER cc_start: 0.7719 (m) cc_final: 0.7170 (t) REVERT: A 573 MET cc_start: 0.1108 (tpp) cc_final: 0.0423 (tmm) REVERT: B 102 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8647 (mmm) REVERT: B 428 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6896 (mmtt) REVERT: B 551 MET cc_start: 0.8410 (ptt) cc_final: 0.8123 (ptm) REVERT: B 741 MET cc_start: 0.7661 (mmm) cc_final: 0.6961 (mtp) REVERT: E 450 MET cc_start: 0.8663 (mmp) cc_final: 0.8260 (mmm) REVERT: F 609 MET cc_start: 0.8046 (ppp) cc_final: 0.7509 (ppp) REVERT: F 649 MET cc_start: 0.7477 (mmp) cc_final: 0.7210 (mmp) REVERT: G 1 MET cc_start: 0.6919 (mtp) cc_final: 0.6701 (mtm) REVERT: G 696 MET cc_start: 0.8368 (tpp) cc_final: 0.8094 (tpp) REVERT: I 102 MET cc_start: 0.8845 (tpp) cc_final: 0.8614 (tpp) REVERT: J 78 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: J 526 ASP cc_start: 0.6835 (m-30) cc_final: 0.6363 (m-30) REVERT: J 741 MET cc_start: 0.7683 (mtt) cc_final: 0.7151 (mtt) REVERT: K 65 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7009 (ptt) REVERT: K 126 TYR cc_start: 0.4751 (t80) cc_final: 0.4412 (t80) REVERT: K 293 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.7409 (t60) REVERT: L 102 MET cc_start: 0.8697 (mmm) cc_final: 0.8336 (tpp) REVERT: M 150 GLU cc_start: 0.8581 (tm-30) cc_final: 0.7902 (tm-30) REVERT: M 385 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.5518 (mtt) REVERT: M 678 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6677 (tt0) REVERT: O 170 LYS cc_start: 0.8311 (tttt) cc_final: 0.7753 (mmtm) REVERT: O 775 MET cc_start: 0.4345 (tpp) cc_final: 0.3382 (ttm) REVERT: O 851 LEU cc_start: 0.6424 (mt) cc_final: 0.6144 (mt) REVERT: P 165 HIS cc_start: 0.6282 (OUTLIER) cc_final: 0.4980 (t70) REVERT: P 430 TYR cc_start: 0.5619 (m-80) cc_final: 0.5149 (m-80) REVERT: P 617 MET cc_start: 0.1128 (tpp) cc_final: -0.0595 (ttm) REVERT: P 758 ARG cc_start: 0.3796 (ttt180) cc_final: 0.3499 (ttm170) REVERT: Q 732 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6369 (mt) REVERT: R 289 MET cc_start: 0.8254 (tpp) cc_final: 0.8020 (tpp) REVERT: R 443 MET cc_start: 0.3627 (tmm) cc_final: 0.3315 (tmm) REVERT: R 539 MET cc_start: 0.0423 (OUTLIER) cc_final: -0.0254 (tmm) REVERT: R 775 MET cc_start: 0.6313 (ptt) cc_final: 0.5044 (ttt) REVERT: S 30 ASP cc_start: 0.5834 (t70) cc_final: 0.5501 (t70) REVERT: S 132 MET cc_start: 0.7001 (mtt) cc_final: 0.6742 (mtt) REVERT: S 425 MET cc_start: 0.5902 (tpt) cc_final: 0.5606 (tpt) REVERT: S 539 MET cc_start: 0.1277 (ptt) cc_final: -0.0961 (tpp) REVERT: T 366 MET cc_start: 0.7407 (ppp) cc_final: 0.6008 (tpp) REVERT: T 510 ILE cc_start: 0.8909 (mm) cc_final: 0.8656 (mt) outliers start: 145 outliers final: 68 residues processed: 876 average time/residue: 0.9714 time to fit residues: 1516.4242 Evaluate side-chains 774 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 697 time to evaluate : 10.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 682 ASP Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 340 HIS Chi-restraints excluded: chain I residue 757 LEU Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 381 LEU Chi-restraints excluded: chain J residue 496 THR Chi-restraints excluded: chain J residue 566 GLU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 293 TRP Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 598 VAL Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 385 MET Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 549 LEU Chi-restraints excluded: chain M residue 678 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 549 LEU Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain P residue 165 HIS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 656 ILE Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 732 LEU Chi-restraints excluded: chain Q residue 745 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 721 ASN Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 199 ILE Chi-restraints excluded: chain T residue 508 VAL Chi-restraints excluded: chain T residue 615 ASN Chi-restraints excluded: chain T residue 811 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1212 optimal weight: 0.9990 chunk 826 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 1083 optimal weight: 0.3980 chunk 600 optimal weight: 3.9990 chunk 1242 optimal weight: 8.9990 chunk 1006 optimal weight: 0.7980 chunk 1 optimal weight: 0.0170 chunk 743 optimal weight: 5.9990 chunk 1306 optimal weight: 40.0000 chunk 367 optimal weight: 10.0000 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 494 HIS ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 124337 Z= 0.145 Angle : 0.498 13.071 168249 Z= 0.253 Chirality : 0.038 0.363 18568 Planarity : 0.003 0.055 21596 Dihedral : 3.937 20.568 16469 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.16 % Allowed : 13.58 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.07), residues: 14986 helix: 1.23 (0.06), residues: 8529 sheet: -1.00 (0.21), residues: 613 loop : -0.86 (0.08), residues: 5844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP Q 738 HIS 0.012 0.001 HIS A 784 PHE 0.030 0.001 PHE P 451 TYR 0.026 0.001 TYR L 433 ARG 0.011 0.000 ARG O 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 774 time to evaluate : 10.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.7956 (mp0) cc_final: 0.7569 (mp0) REVERT: A 280 SER cc_start: 0.7727 (m) cc_final: 0.7203 (t) REVERT: A 336 MET cc_start: 0.5285 (ptp) cc_final: 0.4872 (mpp) REVERT: B 551 MET cc_start: 0.8397 (ptt) cc_final: 0.8104 (ptm) REVERT: B 741 MET cc_start: 0.7552 (mmm) cc_final: 0.7280 (mtp) REVERT: C 573 LEU cc_start: 0.7407 (mp) cc_final: 0.7117 (mt) REVERT: E 450 MET cc_start: 0.8642 (mmp) cc_final: 0.8237 (mmm) REVERT: F 38 TYR cc_start: 0.7782 (t80) cc_final: 0.7214 (t80) REVERT: F 609 MET cc_start: 0.8022 (ppp) cc_final: 0.7473 (ppp) REVERT: F 649 MET cc_start: 0.7451 (mmp) cc_final: 0.7238 (mmp) REVERT: G 696 MET cc_start: 0.8340 (tpp) cc_final: 0.8031 (tpp) REVERT: I 609 MET cc_start: 0.7820 (ptp) cc_final: 0.7497 (ptm) REVERT: J 78 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: J 234 MET cc_start: 0.6197 (tmm) cc_final: 0.5624 (tmm) REVERT: J 526 ASP cc_start: 0.6826 (m-30) cc_final: 0.6416 (m-30) REVERT: K 65 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6985 (ptt) REVERT: K 293 TRP cc_start: 0.8068 (OUTLIER) cc_final: 0.7453 (t60) REVERT: K 741 MET cc_start: 0.7926 (mtp) cc_final: 0.7465 (mtp) REVERT: L 58 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: L 102 MET cc_start: 0.8653 (mmm) cc_final: 0.8299 (tpp) REVERT: L 111 ILE cc_start: 0.9371 (mt) cc_final: 0.9138 (mt) REVERT: L 609 MET cc_start: 0.8249 (ppp) cc_final: 0.7995 (ppp) REVERT: M 385 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.5278 (mtt) REVERT: M 658 GLN cc_start: 0.8219 (mp10) cc_final: 0.7926 (mp10) REVERT: N 366 MET cc_start: 0.7738 (tmm) cc_final: 0.7488 (tmm) REVERT: O 170 LYS cc_start: 0.8367 (tttt) cc_final: 0.7785 (mmtm) REVERT: O 201 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7495 (mt-10) REVERT: O 738 TRP cc_start: 0.6160 (t-100) cc_final: 0.5892 (t-100) REVERT: O 775 MET cc_start: 0.4339 (tpp) cc_final: 0.3961 (mtp) REVERT: P 165 HIS cc_start: 0.6319 (OUTLIER) cc_final: 0.4980 (t70) REVERT: P 617 MET cc_start: 0.0853 (tpp) cc_final: -0.0589 (ttm) REVERT: P 758 ARG cc_start: 0.3752 (ttt180) cc_final: 0.3461 (ttm170) REVERT: Q 78 ARG cc_start: 0.4005 (tmm160) cc_final: 0.2770 (tmm160) REVERT: Q 151 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6082 (pp20) REVERT: Q 732 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6507 (mt) REVERT: R 511 PHE cc_start: 0.6600 (t80) cc_final: 0.6198 (t80) REVERT: R 539 MET cc_start: 0.0144 (OUTLIER) cc_final: -0.0504 (tmm) REVERT: R 775 MET cc_start: 0.6400 (ptt) cc_final: 0.5098 (ttt) REVERT: S 30 ASP cc_start: 0.5813 (t70) cc_final: 0.5490 (t70) REVERT: S 132 MET cc_start: 0.6895 (mtt) cc_final: 0.6642 (mtt) REVERT: S 425 MET cc_start: 0.5766 (tpt) cc_final: 0.5427 (tpt) REVERT: S 539 MET cc_start: 0.1199 (ptt) cc_final: -0.0960 (tpp) REVERT: T 202 GLU cc_start: 0.8059 (pm20) cc_final: 0.7015 (pt0) REVERT: T 510 ILE cc_start: 0.8895 (mm) cc_final: 0.8655 (mt) REVERT: T 842 PHE cc_start: 0.4569 (t80) cc_final: 0.4275 (t80) outliers start: 153 outliers final: 79 residues processed: 889 average time/residue: 0.9744 time to fit residues: 1548.0783 Evaluate side-chains 797 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 710 time to evaluate : 10.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 682 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 741 MET Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 757 LEU Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 566 GLU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 293 TRP Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 598 VAL Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 385 MET Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 549 LEU Chi-restraints excluded: chain M residue 643 LEU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 739 VAL Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain P residue 165 HIS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 509 SER Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 656 ILE Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 732 LEU Chi-restraints excluded: chain Q residue 745 LEU Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain S residue 380 MET Chi-restraints excluded: chain S residue 480 ILE Chi-restraints excluded: chain S residue 721 ASN Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 199 ILE Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 508 VAL Chi-restraints excluded: chain T residue 615 ASN Chi-restraints excluded: chain T residue 796 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 489 optimal weight: 5.9990 chunk 1310 optimal weight: 0.2980 chunk 287 optimal weight: 6.9990 chunk 854 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 1457 optimal weight: 2.9990 chunk 1209 optimal weight: 4.9990 chunk 674 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 482 optimal weight: 5.9990 chunk 764 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 248 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN ** O 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 276 GLN ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 552 ASN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 124337 Z= 0.172 Angle : 0.505 13.939 168249 Z= 0.256 Chirality : 0.038 0.193 18568 Planarity : 0.003 0.056 21596 Dihedral : 3.931 20.782 16469 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.31 % Allowed : 14.35 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.07), residues: 14986 helix: 1.29 (0.06), residues: 8499 sheet: -0.99 (0.22), residues: 608 loop : -0.87 (0.08), residues: 5879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP P 738 HIS 0.016 0.001 HIS A 784 PHE 0.043 0.001 PHE T 741 TYR 0.026 0.001 TYR L 433 ARG 0.010 0.000 ARG O 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 746 time to evaluate : 10.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: A 275 GLU cc_start: 0.7943 (mp0) cc_final: 0.7544 (mp0) REVERT: A 280 SER cc_start: 0.7687 (m) cc_final: 0.7266 (t) REVERT: A 599 LEU cc_start: 0.3766 (tp) cc_final: 0.3481 (mp) REVERT: B 551 MET cc_start: 0.8413 (ptt) cc_final: 0.8154 (ptm) REVERT: B 741 MET cc_start: 0.7495 (mmm) cc_final: 0.7212 (mtt) REVERT: D 234 MET cc_start: 0.6467 (ppp) cc_final: 0.6239 (ppp) REVERT: D 335 LEU cc_start: 0.8619 (tp) cc_final: 0.8352 (tt) REVERT: E 450 MET cc_start: 0.8621 (mmp) cc_final: 0.8289 (mmm) REVERT: E 741 MET cc_start: 0.7931 (ttm) cc_final: 0.7542 (ttm) REVERT: F 38 TYR cc_start: 0.7809 (t80) cc_final: 0.7146 (t80) REVERT: F 366 MET cc_start: 0.7683 (mmp) cc_final: 0.7203 (mmt) REVERT: F 609 MET cc_start: 0.8030 (ppp) cc_final: 0.7528 (ppp) REVERT: G 696 MET cc_start: 0.8322 (tpp) cc_final: 0.8006 (tpp) REVERT: J 78 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: J 526 ASP cc_start: 0.6851 (m-30) cc_final: 0.6451 (m-30) REVERT: K 65 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6998 (ptt) REVERT: K 293 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.7352 (t60) REVERT: K 741 MET cc_start: 0.7954 (mtp) cc_final: 0.7496 (mtp) REVERT: L 58 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: L 102 MET cc_start: 0.8664 (mmm) cc_final: 0.8326 (tpp) REVERT: M 385 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6757 (mtt) REVERT: M 658 GLN cc_start: 0.8212 (mp10) cc_final: 0.7893 (mp10) REVERT: M 675 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8628 (t) REVERT: M 678 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: N 366 MET cc_start: 0.7767 (tmm) cc_final: 0.7506 (tmm) REVERT: O 170 LYS cc_start: 0.8442 (tttt) cc_final: 0.7800 (mmtm) REVERT: O 201 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7520 (mt-10) REVERT: O 256 LEU cc_start: 0.8701 (mt) cc_final: 0.8325 (mt) REVERT: O 738 TRP cc_start: 0.6176 (t-100) cc_final: 0.5904 (t-100) REVERT: P 584 MET cc_start: 0.2224 (mtm) cc_final: 0.1470 (ptp) REVERT: P 617 MET cc_start: 0.0838 (tpp) cc_final: -0.0550 (ttm) REVERT: P 758 ARG cc_start: 0.3777 (ttt180) cc_final: 0.3478 (ttm170) REVERT: Q 151 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6090 (pp20) REVERT: Q 732 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6453 (mt) REVERT: Q 894 TYR cc_start: 0.5755 (OUTLIER) cc_final: 0.5233 (m-10) REVERT: R 289 MET cc_start: 0.8389 (tpp) cc_final: 0.8143 (tpp) REVERT: R 539 MET cc_start: 0.0141 (OUTLIER) cc_final: -0.0589 (tmm) REVERT: R 775 MET cc_start: 0.6354 (ptt) cc_final: 0.5123 (ttt) REVERT: S 30 ASP cc_start: 0.5833 (t70) cc_final: 0.5528 (t70) REVERT: S 132 MET cc_start: 0.6966 (mtt) cc_final: 0.6698 (mtt) REVERT: S 425 MET cc_start: 0.5791 (tpt) cc_final: 0.5390 (tpt) REVERT: S 539 MET cc_start: 0.1329 (ptt) cc_final: -0.0855 (tpp) REVERT: T 202 GLU cc_start: 0.8039 (pm20) cc_final: 0.7072 (pt0) REVERT: T 426 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.6055 (tt) REVERT: T 510 ILE cc_start: 0.8880 (mm) cc_final: 0.8649 (mt) REVERT: T 842 PHE cc_start: 0.4580 (t80) cc_final: 0.4337 (t80) outliers start: 173 outliers final: 108 residues processed: 877 average time/residue: 0.9858 time to fit residues: 1544.2560 Evaluate side-chains 827 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 707 time to evaluate : 10.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 741 MET Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 451 ASP Chi-restraints excluded: chain I residue 757 LEU Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 496 THR Chi-restraints excluded: chain J residue 551 MET Chi-restraints excluded: chain J residue 566 GLU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 293 TRP Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 572 GLU Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 598 VAL Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 102 MET Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 385 MET Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 549 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 678 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 442 LEU Chi-restraints excluded: chain N residue 549 LEU Chi-restraints excluded: chain N residue 739 VAL Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 225 THR Chi-restraints excluded: chain O residue 450 ILE Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 233 VAL Chi-restraints excluded: chain P residue 454 VAL Chi-restraints excluded: chain P residue 509 SER Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 656 ILE Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 732 LEU Chi-restraints excluded: chain Q residue 745 LEU Chi-restraints excluded: chain Q residue 894 TYR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain R residue 569 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 794 HIS Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 380 MET Chi-restraints excluded: chain S residue 480 ILE Chi-restraints excluded: chain S residue 721 ASN Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 199 ILE Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 426 LEU Chi-restraints excluded: chain T residue 508 VAL Chi-restraints excluded: chain T residue 615 ASN Chi-restraints excluded: chain T residue 796 VAL Chi-restraints excluded: chain T residue 811 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1404 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 830 optimal weight: 2.9990 chunk 1064 optimal weight: 0.8980 chunk 824 optimal weight: 9.9990 chunk 1226 optimal weight: 0.0770 chunk 813 optimal weight: 9.9990 chunk 1451 optimal weight: 1.9990 chunk 908 optimal weight: 6.9990 chunk 884 optimal weight: 9.9990 chunk 670 optimal weight: 6.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 787 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN ** O 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 276 GLN ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 22 ASN ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 438 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 124337 Z= 0.186 Angle : 0.516 16.592 168249 Z= 0.261 Chirality : 0.039 0.234 18568 Planarity : 0.003 0.055 21596 Dihedral : 3.950 20.705 16469 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.42 % Allowed : 14.85 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.07), residues: 14986 helix: 1.30 (0.06), residues: 8511 sheet: -1.00 (0.22), residues: 617 loop : -0.87 (0.08), residues: 5858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP Q 738 HIS 0.021 0.001 HIS A 784 PHE 0.034 0.001 PHE A 817 TYR 0.026 0.001 TYR L 433 ARG 0.012 0.000 ARG O 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 741 time to evaluate : 10.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: A 166 LEU cc_start: 0.5739 (OUTLIER) cc_final: 0.5105 (mt) REVERT: A 280 SER cc_start: 0.7656 (m) cc_final: 0.7284 (t) REVERT: A 336 MET cc_start: 0.5483 (ptp) cc_final: 0.4951 (mpp) REVERT: A 599 LEU cc_start: 0.3916 (tp) cc_final: 0.3597 (mp) REVERT: B 551 MET cc_start: 0.8436 (ptt) cc_final: 0.8184 (ptm) REVERT: C 785 GLU cc_start: 0.6651 (mp0) cc_final: 0.6366 (mp0) REVERT: D 234 MET cc_start: 0.6502 (ppp) cc_final: 0.6281 (ppp) REVERT: E 450 MET cc_start: 0.8539 (mmp) cc_final: 0.8272 (mmm) REVERT: E 741 MET cc_start: 0.8018 (ttm) cc_final: 0.7623 (ttm) REVERT: E 757 LEU cc_start: 0.8908 (tp) cc_final: 0.8702 (tp) REVERT: F 366 MET cc_start: 0.7622 (mmp) cc_final: 0.7299 (mmt) REVERT: F 609 MET cc_start: 0.8060 (ppp) cc_final: 0.7549 (ppp) REVERT: G 62 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7244 (mt0) REVERT: G 696 MET cc_start: 0.8310 (tpp) cc_final: 0.7985 (tpp) REVERT: J 78 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: J 526 ASP cc_start: 0.6945 (m-30) cc_final: 0.6655 (m-30) REVERT: J 741 MET cc_start: 0.7788 (mtt) cc_final: 0.7307 (mtt) REVERT: K 65 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7042 (ptt) REVERT: K 293 TRP cc_start: 0.8090 (OUTLIER) cc_final: 0.7380 (t60) REVERT: K 741 MET cc_start: 0.8091 (mtp) cc_final: 0.7657 (mtp) REVERT: L 58 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: L 102 MET cc_start: 0.8671 (mmm) cc_final: 0.8336 (tpp) REVERT: M 385 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6760 (mtt) REVERT: M 675 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8591 (t) REVERT: M 678 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6734 (tt0) REVERT: O 170 LYS cc_start: 0.8482 (tttt) cc_final: 0.7817 (mmtm) REVERT: O 201 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7581 (mt-10) REVERT: O 256 LEU cc_start: 0.8742 (mt) cc_final: 0.8363 (mt) REVERT: O 500 MET cc_start: 0.5036 (mmt) cc_final: 0.4572 (mmt) REVERT: O 738 TRP cc_start: 0.6309 (t-100) cc_final: 0.6013 (t-100) REVERT: P 165 HIS cc_start: 0.6286 (OUTLIER) cc_final: 0.4928 (t70) REVERT: P 212 ASP cc_start: 0.6111 (t0) cc_final: 0.5902 (t0) REVERT: P 617 MET cc_start: 0.0806 (tpp) cc_final: -0.0478 (ttm) REVERT: P 738 TRP cc_start: 0.6968 (t-100) cc_final: 0.5684 (t-100) REVERT: P 758 ARG cc_start: 0.3762 (ttt180) cc_final: 0.3474 (ttm170) REVERT: Q 78 ARG cc_start: 0.3970 (tmm160) cc_final: 0.2775 (tmm160) REVERT: Q 151 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6219 (pp20) REVERT: Q 732 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6621 (mt) REVERT: Q 736 LYS cc_start: 0.6006 (tppt) cc_final: 0.5630 (tppt) REVERT: Q 894 TYR cc_start: 0.5773 (OUTLIER) cc_final: 0.5244 (m-10) REVERT: R 535 TYR cc_start: 0.4577 (t80) cc_final: 0.4218 (t80) REVERT: R 539 MET cc_start: 0.0180 (OUTLIER) cc_final: -0.0578 (tmm) REVERT: R 775 MET cc_start: 0.6308 (ptt) cc_final: 0.5071 (ttt) REVERT: S 30 ASP cc_start: 0.5868 (t70) cc_final: 0.5547 (t70) REVERT: S 132 MET cc_start: 0.7026 (mtt) cc_final: 0.6779 (mtt) REVERT: S 425 MET cc_start: 0.5718 (tpt) cc_final: 0.5271 (tpt) REVERT: S 539 MET cc_start: 0.1510 (ptt) cc_final: -0.0619 (tpp) REVERT: T 202 GLU cc_start: 0.8036 (pm20) cc_final: 0.7150 (pt0) REVERT: T 426 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6038 (tt) REVERT: T 842 PHE cc_start: 0.4790 (t80) cc_final: 0.4445 (t80) outliers start: 188 outliers final: 126 residues processed: 882 average time/residue: 0.9917 time to fit residues: 1560.3292 Evaluate side-chains 841 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 700 time to evaluate : 11.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 741 MET Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 340 HIS Chi-restraints excluded: chain I residue 451 ASP Chi-restraints excluded: chain I residue 757 LEU Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 496 THR Chi-restraints excluded: chain J residue 551 MET Chi-restraints excluded: chain J residue 566 GLU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 293 TRP Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 572 GLU Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 598 VAL Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 385 MET Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 549 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 678 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 442 LEU Chi-restraints excluded: chain N residue 549 LEU Chi-restraints excluded: chain N residue 739 VAL Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 225 THR Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 450 ILE Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 132 MET Chi-restraints excluded: chain P residue 165 HIS Chi-restraints excluded: chain P residue 221 ASP Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 454 VAL Chi-restraints excluded: chain P residue 509 SER Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 656 ILE Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 732 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 745 LEU Chi-restraints excluded: chain Q residue 894 TYR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain R residue 544 ILE Chi-restraints excluded: chain R residue 569 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 794 HIS Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 380 MET Chi-restraints excluded: chain S residue 480 ILE Chi-restraints excluded: chain S residue 721 ASN Chi-restraints excluded: chain S residue 842 PHE Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 199 ILE Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 426 LEU Chi-restraints excluded: chain T residue 508 VAL Chi-restraints excluded: chain T residue 615 ASN Chi-restraints excluded: chain T residue 796 VAL Chi-restraints excluded: chain T residue 811 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 898 optimal weight: 3.9990 chunk 579 optimal weight: 20.0000 chunk 866 optimal weight: 0.9990 chunk 437 optimal weight: 0.0050 chunk 285 optimal weight: 10.0000 chunk 281 optimal weight: 0.4980 chunk 922 optimal weight: 6.9990 chunk 988 optimal weight: 5.9990 chunk 717 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 1140 optimal weight: 30.0000 overall best weight: 2.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 HIS C 787 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 474 HIS ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 597 ASN ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 124337 Z= 0.178 Angle : 0.519 13.193 168249 Z= 0.261 Chirality : 0.039 0.328 18568 Planarity : 0.003 0.053 21596 Dihedral : 3.945 20.697 16469 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.47 % Allowed : 15.23 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.07), residues: 14986 helix: 1.33 (0.06), residues: 8514 sheet: -0.96 (0.22), residues: 601 loop : -0.86 (0.08), residues: 5871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP Q 738 HIS 0.016 0.001 HIS A 784 PHE 0.035 0.001 PHE A 817 TYR 0.027 0.001 TYR K 252 ARG 0.012 0.000 ARG O 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 729 time to evaluate : 10.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: A 166 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5110 (mt) REVERT: A 280 SER cc_start: 0.7639 (m) cc_final: 0.7279 (t) REVERT: A 336 MET cc_start: 0.5508 (ptp) cc_final: 0.4966 (mpp) REVERT: A 599 LEU cc_start: 0.3780 (tp) cc_final: 0.3449 (mp) REVERT: A 743 PHE cc_start: 0.4520 (m-80) cc_final: 0.4279 (m-80) REVERT: D 234 MET cc_start: 0.6479 (ppp) cc_final: 0.6230 (ppp) REVERT: E 450 MET cc_start: 0.8523 (mmp) cc_final: 0.8236 (mmm) REVERT: E 741 MET cc_start: 0.8007 (ttm) cc_final: 0.7612 (ttm) REVERT: E 757 LEU cc_start: 0.8902 (tp) cc_final: 0.8695 (tp) REVERT: F 609 MET cc_start: 0.8123 (ppp) cc_final: 0.7600 (ppp) REVERT: F 649 MET cc_start: 0.7461 (mmp) cc_final: 0.7184 (mmp) REVERT: G 62 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7271 (mt0) REVERT: G 696 MET cc_start: 0.8295 (tpp) cc_final: 0.7975 (tpp) REVERT: J 78 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: J 526 ASP cc_start: 0.6928 (m-30) cc_final: 0.6640 (m-30) REVERT: J 741 MET cc_start: 0.7776 (mtt) cc_final: 0.7299 (mtt) REVERT: K 65 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7064 (ptt) REVERT: K 293 TRP cc_start: 0.8062 (OUTLIER) cc_final: 0.7429 (t60) REVERT: K 741 MET cc_start: 0.8093 (mtp) cc_final: 0.7633 (mtp) REVERT: L 58 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: L 102 MET cc_start: 0.8689 (mmm) cc_final: 0.8365 (tpp) REVERT: M 385 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6663 (mtt) REVERT: M 675 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8568 (t) REVERT: M 678 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6670 (tt0) REVERT: O 170 LYS cc_start: 0.8460 (tttt) cc_final: 0.7786 (mmtm) REVERT: O 201 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7579 (mt-10) REVERT: O 256 LEU cc_start: 0.8710 (mt) cc_final: 0.8308 (mt) REVERT: O 500 MET cc_start: 0.5048 (mmt) cc_final: 0.4594 (mmt) REVERT: O 738 TRP cc_start: 0.6358 (t-100) cc_final: 0.6049 (t-100) REVERT: O 897 LYS cc_start: 0.4087 (mmtt) cc_final: 0.3535 (tttt) REVERT: P 165 HIS cc_start: 0.6366 (OUTLIER) cc_final: 0.4906 (t70) REVERT: P 617 MET cc_start: 0.0913 (tpp) cc_final: -0.0356 (ttm) REVERT: P 758 ARG cc_start: 0.3709 (ttt180) cc_final: 0.3419 (ttm170) REVERT: Q 151 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6145 (pp20) REVERT: Q 443 MET cc_start: 0.4490 (mmm) cc_final: 0.3894 (mmm) REVERT: Q 732 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6620 (mt) REVERT: Q 736 LYS cc_start: 0.6032 (tppt) cc_final: 0.4870 (tppt) REVERT: Q 894 TYR cc_start: 0.5773 (OUTLIER) cc_final: 0.5238 (m-10) REVERT: R 511 PHE cc_start: 0.6582 (t80) cc_final: 0.6242 (t80) REVERT: R 535 TYR cc_start: 0.4599 (t80) cc_final: 0.4211 (t80) REVERT: R 539 MET cc_start: 0.0144 (OUTLIER) cc_final: -0.0585 (tmm) REVERT: R 775 MET cc_start: 0.6307 (ptt) cc_final: 0.5140 (ttt) REVERT: S 30 ASP cc_start: 0.5868 (t70) cc_final: 0.5543 (t70) REVERT: S 132 MET cc_start: 0.7035 (mtt) cc_final: 0.6792 (mtt) REVERT: S 425 MET cc_start: 0.5688 (tpt) cc_final: 0.5225 (tpt) REVERT: S 539 MET cc_start: 0.1515 (ptt) cc_final: -0.0609 (tpp) REVERT: T 202 GLU cc_start: 0.8028 (pm20) cc_final: 0.7252 (pt0) REVERT: T 366 MET cc_start: 0.7912 (ppp) cc_final: 0.7501 (ppp) REVERT: T 765 MET cc_start: 0.2242 (mmt) cc_final: 0.1953 (mmp) REVERT: T 842 PHE cc_start: 0.4910 (t80) cc_final: 0.4521 (t80) outliers start: 194 outliers final: 139 residues processed: 881 average time/residue: 1.0205 time to fit residues: 1572.0446 Evaluate side-chains 855 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 702 time to evaluate : 9.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 741 MET Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 551 MET Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 252 TYR Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 741 MET Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 340 HIS Chi-restraints excluded: chain I residue 451 ASP Chi-restraints excluded: chain I residue 757 LEU Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 496 THR Chi-restraints excluded: chain J residue 566 GLU Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 293 TRP Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 572 GLU Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 598 VAL Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 385 MET Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 549 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 678 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 442 LEU Chi-restraints excluded: chain N residue 507 ILE Chi-restraints excluded: chain N residue 549 LEU Chi-restraints excluded: chain N residue 649 MET Chi-restraints excluded: chain N residue 739 VAL Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 225 THR Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 450 ILE Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain P residue 132 MET Chi-restraints excluded: chain P residue 165 HIS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 233 VAL Chi-restraints excluded: chain P residue 332 THR Chi-restraints excluded: chain P residue 509 SER Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 656 ILE Chi-restraints excluded: chain P residue 657 VAL Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain Q residue 17 ASN Chi-restraints excluded: chain Q residue 140 TYR Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 732 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 745 LEU Chi-restraints excluded: chain Q residue 894 TYR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain R residue 544 ILE Chi-restraints excluded: chain R residue 569 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 794 HIS Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 280 SER Chi-restraints excluded: chain S residue 380 MET Chi-restraints excluded: chain S residue 480 ILE Chi-restraints excluded: chain S residue 721 ASN Chi-restraints excluded: chain S residue 842 PHE Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 199 ILE Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 508 VAL Chi-restraints excluded: chain T residue 615 ASN Chi-restraints excluded: chain T residue 796 VAL Chi-restraints excluded: chain T residue 811 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 1320 optimal weight: 6.9990 chunk 1390 optimal weight: 8.9990 chunk 1268 optimal weight: 3.9990 chunk 1352 optimal weight: 20.0000 chunk 814 optimal weight: 9.9990 chunk 589 optimal weight: 0.9990 chunk 1062 optimal weight: 30.0000 chunk 415 optimal weight: 8.9990 chunk 1222 optimal weight: 40.0000 chunk 1279 optimal weight: 9.9990 chunk 1347 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 194 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 GLN ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 248 ASN ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 570 HIS M 789 ASN N 114 HIS ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 346 GLN P 384 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 560 ASN ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 912 ASN ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 124337 Z= 0.297 Angle : 0.599 12.843 168249 Z= 0.301 Chirality : 0.041 0.350 18568 Planarity : 0.004 0.062 21596 Dihedral : 4.210 21.723 16469 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.49 % Allowed : 15.52 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.07), residues: 14986 helix: 1.11 (0.06), residues: 8566 sheet: -1.13 (0.22), residues: 608 loop : -0.95 (0.08), residues: 5812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP Q 738 HIS 0.013 0.001 HIS B 384 PHE 0.033 0.002 PHE A 817 TYR 0.029 0.002 TYR L 38 ARG 0.023 0.000 ARG O 418 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 705 time to evaluate : 9.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: A 280 SER cc_start: 0.7706 (m) cc_final: 0.7343 (t) REVERT: A 599 LEU cc_start: 0.3954 (tp) cc_final: 0.3517 (mp) REVERT: A 702 ASP cc_start: 0.1027 (OUTLIER) cc_final: 0.0592 (t70) REVERT: A 743 PHE cc_start: 0.4500 (m-80) cc_final: 0.4242 (m-80) REVERT: B 102 MET cc_start: 0.8898 (tpp) cc_final: 0.8585 (mmm) REVERT: D 234 MET cc_start: 0.6485 (ppp) cc_final: 0.6216 (ppp) REVERT: E 741 MET cc_start: 0.8159 (ttm) cc_final: 0.7752 (ttm) REVERT: F 609 MET cc_start: 0.8138 (ppp) cc_final: 0.7778 (ppp) REVERT: I 609 MET cc_start: 0.7957 (ptp) cc_final: 0.7748 (ptm) REVERT: J 78 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: J 741 MET cc_start: 0.7789 (mtt) cc_final: 0.7357 (mtt) REVERT: K 65 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7351 (ptt) REVERT: K 293 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7439 (t60) REVERT: K 741 MET cc_start: 0.8178 (mtp) cc_final: 0.7703 (mtp) REVERT: L 58 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: L 102 MET cc_start: 0.8714 (mmm) cc_final: 0.8420 (tpp) REVERT: L 609 MET cc_start: 0.8333 (ppp) cc_final: 0.7314 (ppp) REVERT: M 150 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7379 (tm-30) REVERT: M 385 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6720 (mtt) REVERT: M 612 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8831 (mt) REVERT: M 675 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8750 (t) REVERT: M 678 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: M 693 MET cc_start: 0.9130 (mmm) cc_final: 0.8684 (mmm) REVERT: O 170 LYS cc_start: 0.8527 (tttt) cc_final: 0.7829 (mmtm) REVERT: O 201 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7519 (mp0) REVERT: O 256 LEU cc_start: 0.8769 (mt) cc_final: 0.8382 (mt) REVERT: O 366 MET cc_start: 0.6376 (ppp) cc_final: 0.5905 (ttt) REVERT: P 165 HIS cc_start: 0.6294 (OUTLIER) cc_final: 0.5234 (t70) REVERT: P 212 ASP cc_start: 0.6020 (t0) cc_final: 0.5743 (t0) REVERT: P 313 MET cc_start: 0.6138 (mmm) cc_final: 0.5847 (mmp) REVERT: P 617 MET cc_start: 0.0398 (tpp) cc_final: -0.1002 (ttm) REVERT: P 758 ARG cc_start: 0.3708 (ttt180) cc_final: 0.3384 (ttm170) REVERT: P 792 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5741 (tt) REVERT: Q 732 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6654 (mt) REVERT: Q 894 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.5284 (m-10) REVERT: R 539 MET cc_start: 0.0398 (OUTLIER) cc_final: -0.0320 (tmm) REVERT: R 775 MET cc_start: 0.6274 (ptt) cc_final: 0.5125 (ttt) REVERT: S 132 MET cc_start: 0.7351 (mtt) cc_final: 0.7123 (mtt) REVERT: S 354 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6381 (pm20) REVERT: S 391 TYR cc_start: 0.6952 (t80) cc_final: 0.6612 (t80) REVERT: S 425 MET cc_start: 0.5717 (tpt) cc_final: 0.5273 (tpt) REVERT: S 539 MET cc_start: 0.1996 (ptt) cc_final: -0.0434 (tpp) REVERT: T 202 GLU cc_start: 0.8056 (pm20) cc_final: 0.7330 (pt0) REVERT: T 366 MET cc_start: 0.7839 (ppp) cc_final: 0.7568 (ppp) REVERT: T 539 MET cc_start: 0.2243 (tpt) cc_final: 0.1872 (tpt) outliers start: 197 outliers final: 144 residues processed: 858 average time/residue: 0.9517 time to fit residues: 1458.2735 Evaluate side-chains 836 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 676 time to evaluate : 10.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 682 ASP Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 65 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 730 LEU Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 741 MET Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 340 HIS Chi-restraints excluded: chain I residue 757 LEU Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 481 CYS Chi-restraints excluded: chain J residue 496 THR Chi-restraints excluded: chain J residue 551 MET Chi-restraints excluded: chain J residue 566 GLU Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 293 TRP Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 572 GLU Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 598 VAL Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 385 MET Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 612 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 678 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 442 LEU Chi-restraints excluded: chain N residue 507 ILE Chi-restraints excluded: chain N residue 549 LEU Chi-restraints excluded: chain N residue 649 MET Chi-restraints excluded: chain N residue 739 VAL Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 225 THR Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 450 ILE Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 132 MET Chi-restraints excluded: chain P residue 165 HIS Chi-restraints excluded: chain P residue 221 ASP Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 233 VAL Chi-restraints excluded: chain P residue 332 THR Chi-restraints excluded: chain P residue 454 VAL Chi-restraints excluded: chain P residue 509 SER Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 657 VAL Chi-restraints excluded: chain P residue 792 LEU Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain Q residue 17 ASN Chi-restraints excluded: chain Q residue 83 THR Chi-restraints excluded: chain Q residue 140 TYR Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 732 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 745 LEU Chi-restraints excluded: chain Q residue 894 TYR Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 450 ILE Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain R residue 544 ILE Chi-restraints excluded: chain R residue 569 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 280 SER Chi-restraints excluded: chain S residue 354 GLU Chi-restraints excluded: chain S residue 380 MET Chi-restraints excluded: chain S residue 480 ILE Chi-restraints excluded: chain S residue 721 ASN Chi-restraints excluded: chain S residue 842 PHE Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 199 ILE Chi-restraints excluded: chain T residue 225 THR Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 508 VAL Chi-restraints excluded: chain T residue 615 ASN Chi-restraints excluded: chain T residue 796 VAL Chi-restraints excluded: chain T residue 811 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 888 optimal weight: 7.9990 chunk 1430 optimal weight: 8.9990 chunk 873 optimal weight: 0.7980 chunk 678 optimal weight: 2.9990 chunk 994 optimal weight: 2.9990 chunk 1500 optimal weight: 20.0000 chunk 1380 optimal weight: 8.9990 chunk 1194 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 922 optimal weight: 10.0000 chunk 732 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN D 194 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN ** G 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 435 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 796 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 GLN ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 513 GLN S 751 GLN ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 124337 Z= 0.170 Angle : 0.538 13.446 168249 Z= 0.269 Chirality : 0.039 0.341 18568 Planarity : 0.003 0.064 21596 Dihedral : 4.057 21.439 16469 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.27 % Allowed : 15.96 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.07), residues: 14986 helix: 1.28 (0.06), residues: 8533 sheet: -0.87 (0.24), residues: 531 loop : -0.91 (0.08), residues: 5922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP Q 738 HIS 0.011 0.001 HIS A 784 PHE 0.031 0.001 PHE T 741 TYR 0.028 0.001 TYR F 679 ARG 0.016 0.000 ARG O 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 29972 Ramachandran restraints generated. 14986 Oldfield, 0 Emsley, 14986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 732 time to evaluate : 10.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: A 280 SER cc_start: 0.7777 (m) cc_final: 0.7380 (t) REVERT: A 599 LEU cc_start: 0.3611 (tp) cc_final: 0.3291 (mp) REVERT: A 743 PHE cc_start: 0.4480 (m-80) cc_final: 0.4243 (m-80) REVERT: B 102 MET cc_start: 0.8593 (tpp) cc_final: 0.8312 (mmm) REVERT: B 649 MET cc_start: 0.6980 (pmm) cc_final: 0.5911 (pmm) REVERT: D 234 MET cc_start: 0.6569 (ppp) cc_final: 0.6301 (ppp) REVERT: E 741 MET cc_start: 0.8037 (ttm) cc_final: 0.7645 (ttm) REVERT: F 609 MET cc_start: 0.8091 (ppp) cc_final: 0.7737 (ppp) REVERT: G 452 MET cc_start: 0.6873 (ppp) cc_final: 0.6661 (tmm) REVERT: J 78 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: J 526 ASP cc_start: 0.6751 (m-30) cc_final: 0.6337 (m-30) REVERT: J 741 MET cc_start: 0.7822 (mtt) cc_final: 0.7399 (mtt) REVERT: K 65 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7170 (ptt) REVERT: K 293 TRP cc_start: 0.8035 (OUTLIER) cc_final: 0.7408 (t60) REVERT: K 741 MET cc_start: 0.8145 (mtp) cc_final: 0.7742 (mtp) REVERT: L 58 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: L 102 MET cc_start: 0.8709 (mmm) cc_final: 0.8390 (tpp) REVERT: M 385 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6486 (mtt) REVERT: M 675 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8623 (t) REVERT: M 678 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6703 (tt0) REVERT: O 170 LYS cc_start: 0.8538 (tttt) cc_final: 0.7837 (mmtm) REVERT: O 201 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7527 (mt-10) REVERT: O 366 MET cc_start: 0.6347 (ppp) cc_final: 0.5919 (ttt) REVERT: O 738 TRP cc_start: 0.6460 (t-100) cc_final: 0.6134 (t-100) REVERT: P 165 HIS cc_start: 0.6295 (OUTLIER) cc_final: 0.4999 (t70) REVERT: P 313 MET cc_start: 0.6192 (mmm) cc_final: 0.5922 (mmp) REVERT: P 617 MET cc_start: 0.0175 (tpp) cc_final: -0.1039 (ttm) REVERT: P 758 ARG cc_start: 0.3680 (ttt180) cc_final: 0.3360 (ttm170) REVERT: Q 151 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6158 (pp20) REVERT: Q 894 TYR cc_start: 0.5794 (OUTLIER) cc_final: 0.5339 (m-10) REVERT: R 535 TYR cc_start: 0.4728 (t80) cc_final: 0.4353 (t80) REVERT: R 539 MET cc_start: 0.0198 (OUTLIER) cc_final: -0.0555 (tmm) REVERT: R 775 MET cc_start: 0.6266 (ptt) cc_final: 0.5191 (ttt) REVERT: S 354 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6421 (pm20) REVERT: S 391 TYR cc_start: 0.6898 (t80) cc_final: 0.6593 (t80) REVERT: S 425 MET cc_start: 0.5641 (tpt) cc_final: 0.5158 (tpt) REVERT: T 202 GLU cc_start: 0.8032 (pm20) cc_final: 0.7297 (pt0) REVERT: T 366 MET cc_start: 0.7847 (ppp) cc_final: 0.7529 (ppp) REVERT: T 765 MET cc_start: 0.2183 (mmt) cc_final: 0.1891 (mmp) REVERT: T 842 PHE cc_start: 0.4686 (t80) cc_final: 0.4464 (t80) outliers start: 168 outliers final: 129 residues processed: 864 average time/residue: 0.9665 time to fit residues: 1486.3954 Evaluate side-chains 843 residues out of total 13371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 702 time to evaluate : 10.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 770 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 496 THR Chi-restraints excluded: chain C residue 578 SER Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 583 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 507 ILE Chi-restraints excluded: chain E residue 786 VAL Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 234 MET Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 559 ASP Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 768 LEU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 340 HIS Chi-restraints excluded: chain I residue 757 LEU Chi-restraints excluded: chain I residue 792 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 496 THR Chi-restraints excluded: chain J residue 551 MET Chi-restraints excluded: chain J residue 566 GLU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 133 TYR Chi-restraints excluded: chain K residue 250 ARG Chi-restraints excluded: chain K residue 293 TRP Chi-restraints excluded: chain K residue 342 HIS Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 569 SER Chi-restraints excluded: chain K residue 572 GLU Chi-restraints excluded: chain L residue 58 GLN Chi-restraints excluded: chain L residue 70 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 598 VAL Chi-restraints excluded: chain L residue 675 VAL Chi-restraints excluded: chain L residue 711 THR Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 92 LEU Chi-restraints excluded: chain M residue 260 ILE Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 385 MET Chi-restraints excluded: chain M residue 496 THR Chi-restraints excluded: chain M residue 549 LEU Chi-restraints excluded: chain M residue 675 VAL Chi-restraints excluded: chain M residue 678 GLU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain N residue 130 TRP Chi-restraints excluded: chain N residue 196 ASP Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain N residue 442 LEU Chi-restraints excluded: chain N residue 507 ILE Chi-restraints excluded: chain N residue 549 LEU Chi-restraints excluded: chain N residue 649 MET Chi-restraints excluded: chain N residue 739 VAL Chi-restraints excluded: chain O residue 132 MET Chi-restraints excluded: chain O residue 225 THR Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 450 ILE Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 595 THR Chi-restraints excluded: chain O residue 765 MET Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 132 MET Chi-restraints excluded: chain P residue 165 HIS Chi-restraints excluded: chain P residue 222 ASP Chi-restraints excluded: chain P residue 233 VAL Chi-restraints excluded: chain P residue 332 THR Chi-restraints excluded: chain P residue 454 VAL Chi-restraints excluded: chain P residue 509 SER Chi-restraints excluded: chain P residue 654 THR Chi-restraints excluded: chain P residue 657 VAL Chi-restraints excluded: chain P residue 915 THR Chi-restraints excluded: chain Q residue 17 ASN Chi-restraints excluded: chain Q residue 140 TYR Chi-restraints excluded: chain Q residue 248 VAL Chi-restraints excluded: chain Q residue 293 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 745 LEU Chi-restraints excluded: chain Q residue 894 TYR Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 539 MET Chi-restraints excluded: chain R residue 544 ILE Chi-restraints excluded: chain R residue 569 VAL Chi-restraints excluded: chain R residue 754 THR Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain S residue 133 VAL Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 280 SER Chi-restraints excluded: chain S residue 354 GLU Chi-restraints excluded: chain S residue 380 MET Chi-restraints excluded: chain S residue 480 ILE Chi-restraints excluded: chain S residue 721 ASN Chi-restraints excluded: chain S residue 842 PHE Chi-restraints excluded: chain T residue 45 ILE Chi-restraints excluded: chain T residue 144 ASN Chi-restraints excluded: chain T residue 160 LEU Chi-restraints excluded: chain T residue 199 ILE Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 508 VAL Chi-restraints excluded: chain T residue 796 VAL Chi-restraints excluded: chain T residue 811 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1506 random chunks: chunk 949 optimal weight: 9.9990 chunk 1272 optimal weight: 10.0000 chunk 366 optimal weight: 1.9990 chunk 1101 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 1196 optimal weight: 9.9990 chunk 500 optimal weight: 9.9990 chunk 1228 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 220 optimal weight: 0.0070 overall best weight: 5.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 ASN D 7 ASN D 194 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 445 GLN J 570 HIS ** K 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 668 GLN ** O 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 839 HIS ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 384 GLN ** P 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.102166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.084622 restraints weight = 429566.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.083582 restraints weight = 396357.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.083771 restraints weight = 361955.936| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 124337 Z= 0.310 Angle : 0.614 14.211 168249 Z= 0.308 Chirality : 0.041 0.315 18568 Planarity : 0.004 0.059 21596 Dihedral : 4.280 22.091 16469 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.29 % Allowed : 16.12 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.07), residues: 14986 helix: 1.05 (0.06), residues: 8567 sheet: -1.07 (0.23), residues: 528 loop : -1.01 (0.08), residues: 5891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP P 716 HIS 0.013 0.001 HIS B 384 PHE 0.031 0.002 PHE R 240 TYR 0.032 0.002 TYR L 55 ARG 0.015 0.000 ARG O 418 =============================================================================== Job complete usr+sys time: 23833.64 seconds wall clock time: 420 minutes 46.77 seconds (25246.77 seconds total)